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HEADER HYDROLASE 05-SEP-14 4UZJ
TITLE STRUCTURE OF A WNT DEACYLASE REGULATOR FROM DROSOPHILA -
TITLE 2 CRYSTAL FORM I - 2.4A
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: NOTUM;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: RESIDUES 82-415,598-617;
COMPND 5 SYNONYM: NOTUM PROTEIN, WINGFUL;
COMPND 6 EC: 3.1.1.1;
COMPND 7 ENGINEERED: YES;
COMPND 8 OTHER_DETAILS: GLYCOSYLATED AT N95
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER;
SOURCE 3 ORGANISM_COMMON: FRUIT FLY;
SOURCE 4 ORGANISM_TAXID: 7227;
SOURCE 5 EXPRESSION_SYSTEM: HOMO SAPIENS;
SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606;
SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293T;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHLSEC
KEYWDS HYDROLASE, ESTERASE, EXTRACELLULAR, ALPHA/BETA HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.ZEBISCH,E.Y.JONES
REVDAT 1 25-FEB-15 4UZJ 0
JRNL AUTH S.KAKUGAWA,P.F.LANGTON,M.ZEBISCH,S.A.HOWELL,T.-H.CHANG,
JRNL AUTH 2 Y.LIU,T.FEIZI,G.BINEVA,N.O'REILLY,A.P.SNIJDERS,E.Y.JONES,
JRNL AUTH 3 J.-P.VINCENT
JRNL TITL NOTUM DEACYLATES WNT PROTEINS TO SUPPRESS SIGNALLING
JRNL TITL 2 ACTIVITY
JRNL REF NATURE 2015
JRNL REFN ESSN 1476-4687
JRNL DOI 10.1038/NATURE14259
REMARK 2
REMARK 2 RESOLUTION. 2.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0073
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,
REMARK 3 STEINER,NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 83.77
REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.71
REMARK 3 NUMBER OF REFLECTIONS : 29879
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.19842
REMARK 3 R VALUE (WORKING SET) : 0.19685
REMARK 3 FREE R VALUE : 0.24338
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.3
REMARK 3 FREE R VALUE TEST SET COUNT : 1030
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.400
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.462
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2184
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.43
REMARK 3 BIN R VALUE (WORKING SET) : 0.323
REMARK 3 BIN FREE R VALUE SET COUNT : 82
REMARK 3 BIN FREE R VALUE : 0.356
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5469
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 14
REMARK 3 SOLVENT ATOMS : 14
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 53
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.106
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.07
REMARK 3 B22 (A**2) : -3.79
REMARK 3 B33 (A**2) : 1.87
REMARK 3 B12 (A**2) : 0.00
REMARK 3 B13 (A**2) : 3.07
REMARK 3 B23 (A**2) : 0.00
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.401
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.254
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.217
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.748
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5659 ; 0.011 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 5238 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7701 ; 1.494 ; 1.935
REMARK 3 BOND ANGLES OTHERS (DEGREES): 12013 ; 0.813 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 675 ; 6.313 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 260 ;32.990 ;22.154
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 906 ;16.448 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 54 ;19.030 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 803 ; 0.084 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6346 ; 0.006 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1412 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2718 ; 2.355 ; 3.646
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2717 ; 2.354 ; 3.645
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3387 ; 3.741 ; 5.461
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2941 ; 3.031 ; 4.014
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 2
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B 85 B 1617
REMARK 3 ORIGIN FOR THE GROUP (A): -22.6478 -31.4975 25.3906
REMARK 3 T TENSOR
REMARK 3 T11: 0.2162 T22: 0.4629
REMARK 3 T33: 0.1085 T12: 0.0402
REMARK 3 T13: -0.0914 T23: 0.0185
REMARK 3 L TENSOR
REMARK 3 L11: 2.0332 L22: 0.9626
REMARK 3 L33: 1.4697 L12: -0.3561
REMARK 3 L13: 0.1502 L23: -1.1702
REMARK 3 S TENSOR
REMARK 3 S11: -0.0323 S12: 0.0504 S13: -0.0237
REMARK 3 S21: -0.2342 S22: -0.0017 S23: -0.0017
REMARK 3 S31: 0.3097 S32: 0.0153 S33: 0.0340
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 84 A 617
REMARK 3 ORIGIN FOR THE GROUP (A): -2.8440 7.5378 13.1459
REMARK 3 T TENSOR
REMARK 3 T11: 0.1659 T22: 0.5304
REMARK 3 T33: 0.0881 T12: 0.0309
REMARK 3 T13: -0.1043 T23: 0.0271
REMARK 3 L TENSOR
REMARK 3 L11: 2.2294 L22: 1.0780
REMARK 3 L33: 0.8019 L12: 1.1094
REMARK 3 L13: 0.4103 L23: -0.3191
REMARK 3 S TENSOR
REMARK 3 S11: -0.1059 S12: -0.1709 S13: 0.0217
REMARK 3 S21: -0.0349 S22: 0.0705 S23: 0.0982
REMARK 3 S31: -0.1905 S32: 0.0064 S33: 0.0354
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE
REMARK 3 RIDING POSITIONS.
REMARK 4
REMARK 4 4UZJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-SEP-14.
REMARK 100 THE PDBE ID CODE IS EBI-61704.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 28-FEB-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I02
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL (PILATUS)
REMARK 200 DETECTOR MANUFACTURER : DECTRIS
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30929
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.40
REMARK 200 RESOLUTION RANGE LOW (A) : 58.00
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9
REMARK 200 DATA REDUNDANCY : 3.0
REMARK 200 R MERGE (I) : 0.05
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 13.80
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NONE
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 49
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.4
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.12 M ALCOHOLS, 0.1 M
REMARK 280 TRIS/BICINE 8.5, 30 % EDO_P8K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 40.69700
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLU A 81
REMARK 465 THR A 82
REMARK 465 GLY A 83
REMARK 465 GLU A 193
REMARK 465 PRO A 194
REMARK 465 ASP A 195
REMARK 465 THR A 196
REMARK 465 SER A 197
REMARK 465 ASP A 198
REMARK 465 ARG A 199
REMARK 465 GLU A 200
REMARK 465 ASN A 201
REMARK 465 GLY A 416
REMARK 465 ASN A 417
REMARK 465 ASN A 418
REMARK 465 ASN A 419
REMARK 465 GLY A 420
REMARK 465 CYS A 598
REMARK 465 GLY A 599
REMARK 465 GLY A 618
REMARK 465 THR A 619
REMARK 465 HIS A 620
REMARK 465 HIS A 621
REMARK 465 HIS A 622
REMARK 465 HIS A 623
REMARK 465 HIS A 624
REMARK 465 HIS A 625
REMARK 465 HIS A 626
REMARK 465 HIS A 627
REMARK 465 HIS A 628
REMARK 465 HIS A 629
REMARK 465 GLU B 81
REMARK 465 THR B 82
REMARK 465 GLY B 83
REMARK 465 ASP B 84
REMARK 465 ASP B 195
REMARK 465 THR B 196
REMARK 465 SER B 197
REMARK 465 ASP B 198
REMARK 465 ARG B 199
REMARK 465 GLU B 200
REMARK 465 ASN B 201
REMARK 465 SER B 202
REMARK 465 GLY B 416
REMARK 465 ASN B 417
REMARK 465 ASN B 418
REMARK 465 ASN B 419
REMARK 465 GLY B 420
REMARK 465 CYS B 598
REMARK 465 GLY B 599
REMARK 465 THR B 617
REMARK 465 GLY B 618
REMARK 465 THR B 619
REMARK 465 HIS B 620
REMARK 465 HIS B 621
REMARK 465 HIS B 622
REMARK 465 HIS B 623
REMARK 465 HIS B 624
REMARK 465 HIS B 625
REMARK 465 HIS B 626
REMARK 465 HIS B 627
REMARK 465 HIS B 628
REMARK 465 HIS B 629
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 SER A 202 OG
REMARK 470 LEU A 600 CG CD1 CD2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG A 155 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 ARG A 155 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 ARG A 265 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 ARG A 265 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES
REMARK 500 ARG B 265 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 ARG B 265 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 TRP A 127 -136.34 -121.21
REMARK 500 LEU A 142 51.82 -171.99
REMARK 500 ASN A 173 32.92 -99.49
REMARK 500 SER A 237 -110.29 52.13
REMARK 500 ASN A 256 -62.87 -100.91
REMARK 500 SER A 286 -58.92 -29.40
REMARK 500 TRP A 314 -12.21 -46.94
REMARK 500 PHE A 337 68.85 -114.80
REMARK 500 VAL A 386 -33.80 -158.18
REMARK 500 SER B 116 142.35 -36.91
REMARK 500 TRP B 127 -138.57 -123.64
REMARK 500 LEU B 142 55.74 -154.02
REMARK 500 SER B 237 -112.47 52.28
REMARK 500 ASN B 256 -69.49 -101.82
REMARK 500 SER B 286 -63.73 -26.39
REMARK 500 PHE B 337 68.64 -119.25
REMARK 500 VAL B 386 -34.32 -155.87
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR MONO-SACCHARIDE
REMARK 800 NAG B1617 BOUND TO ASN B 95
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4UYU RELATED DB: PDB
REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I
REMARK 900 IODIDE COMPLEX - 2.3A
REMARK 900 RELATED ID: 4UYW RELATED DB: PDB
REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I
REMARK 900 HEPARIN FRAGMENT COMPLEX - 1.7A
REMARK 900 RELATED ID: 4UYZ RELATED DB: PDB
REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM II
REMARK 900 - 2.8A
REMARK 900 RELATED ID: 4UZ1 RELATED DB: PDB
REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM
REMARK 900 III - 1.4A
REMARK 900 RELATED ID: 4UZ5 RELATED DB: PDB
REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM IV
REMARK 900 - 2.1A
REMARK 900 RELATED ID: 4UZ6 RELATED DB: PDB
REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM V
REMARK 900 - SOS COMPLEX - 1.9A
REMARK 900 RELATED ID: 4UZ7 RELATED DB: PDB
REMARK 900 STRUCTURE OF THE WNT DEACETYLASE NOTUM - CRYSTAL FORM
REMARK 900 VII - SOS COMPLEX - 2.2A
REMARK 900 RELATED ID: 4UZ9 RELATED DB: PDB
REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM
REMARK 900 VII - SOS COMPLEX - 2.2A
REMARK 900 RELATED ID: 4UZA RELATED DB: PDB
REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM
REMARK 900 VIII - PHOSPHATE COMPLEX - 2.4A
REMARK 900 RELATED ID: 4UZK RELATED DB: PDB
REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM FROM DROSOPHILA -
REMARK 900 CRYSTAL FORM II - 1.9A
REMARK 900 RELATED ID: 4UZL RELATED DB: PDB
REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I
REMARK 900 MYRISTOLEATE COMPLEX - 2.1A
REMARK 900 RELATED ID: 4UZQ RELATED DB: PDB
REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH
REMARK 900 O-PALMITOLEOYL SERINE - CRYSTAL FORM IX - 1.5A
REMARK 900 RELATED ID: 4WBH RELATED DB: PDB
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 R416-K597 REPLACED BY GNNNG LINKER
DBREF 4UZJ A 86 415 UNP Q9VUX3 Q9VUX3_DROME 86 415
DBREF 4UZJ A 598 617 UNP Q9VUX3 Q9VUX3_DROME 598 617
DBREF 4UZJ B 86 415 UNP Q9VUX3 Q9VUX3_DROME 86 415
DBREF 4UZJ B 598 617 UNP Q9VUX3 Q9VUX3_DROME 598 617
SEQADV 4UZJ GLU A 81 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ THR A 82 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ GLY A 83 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ ASP A 84 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS A 85 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ GLY A 416 UNP Q9VUX3 LINKER
SEQADV 4UZJ ASN A 417 UNP Q9VUX3 LINKER
SEQADV 4UZJ ASN A 418 UNP Q9VUX3 LINKER
SEQADV 4UZJ ASN A 419 UNP Q9VUX3 LINKER
SEQADV 4UZJ GLY A 420 UNP Q9VUX3 LINKER
SEQADV 4UZJ GLY A 618 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ THR A 619 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS A 620 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS A 621 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS A 622 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS A 623 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS A 624 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS A 625 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS A 626 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS A 627 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS A 628 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS A 629 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ GLU B 81 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ THR B 82 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ GLY B 83 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ ASP B 84 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS B 85 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ GLY B 416 UNP Q9VUX3 LINKER
SEQADV 4UZJ ASN B 417 UNP Q9VUX3 LINKER
SEQADV 4UZJ ASN B 418 UNP Q9VUX3 LINKER
SEQADV 4UZJ ASN B 419 UNP Q9VUX3 LINKER
SEQADV 4UZJ GLY B 420 UNP Q9VUX3 LINKER
SEQADV 4UZJ GLY B 618 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ THR B 619 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS B 620 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS B 621 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS B 622 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS B 623 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS B 624 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS B 625 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS B 626 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS B 627 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS B 628 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZJ HIS B 629 UNP Q9VUX3 EXPRESSION TAG
SEQRES 1 A 372 GLU THR GLY ASP HIS ARG SER LEU LYS ARG ALA ASN LEU
SEQRES 2 A 372 ALA ASN THR SER ILE THR CYS ASN ASP GLY SER HIS ALA
SEQRES 3 A 372 GLY PHE TYR LEU ARG LYS HIS PRO SER SER LYS LYS TRP
SEQRES 4 A 372 ILE VAL LEU LEU GLU GLY GLY TRP HIS CYS PHE ASP VAL
SEQRES 5 A 372 ARG SER CYS ARG SER ARG TRP MET ARG LEU ARG HIS LEU
SEQRES 6 A 372 MET THR SER SER GLN TRP PRO GLU THR ARG ASP VAL GLY
SEQRES 7 A 372 GLY ILE LEU SER PRO HIS PRO GLU GLU ASN PRO TYR TRP
SEQRES 8 A 372 HIS ASN ALA ASN HIS VAL LEU ILE PRO TYR CYS SER SER
SEQRES 9 A 372 ASP SER TRP SER GLY THR ARG THR GLU PRO ASP THR SER
SEQRES 10 A 372 ASP ARG GLU ASN SER TRP ARG PHE MET GLY ALA LEU ILE
SEQRES 11 A 372 LEU ARG GLN VAL ILE ALA GLU LEU ILE PRO VAL GLY LEU
SEQRES 12 A 372 GLY ARG VAL PRO GLY GLY GLU LEU MET LEU VAL GLY SER
SEQRES 13 A 372 SER ALA GLY GLY MET GLY VAL MET LEU ASN LEU ASP ARG
SEQRES 14 A 372 ILE ARG ASP PHE LEU VAL ASN GLU LYS LYS LEU GLN ILE
SEQRES 15 A 372 THR VAL ARG GLY VAL SER ASP SER GLY TRP PHE LEU ASP
SEQRES 16 A 372 ARG GLU PRO TYR THR PRO ALA ALA VAL ALA SER ASN GLU
SEQRES 17 A 372 ALA VAL ARG GLN GLY TRP LYS LEU TRP GLN GLY LEU LEU
SEQRES 18 A 372 PRO GLU GLU CYS THR LYS SER TYR PRO THR GLU PRO TRP
SEQRES 19 A 372 ARG CYS TYR TYR GLY TYR ARG LEU TYR PRO THR LEU LYS
SEQRES 20 A 372 THR PRO LEU PHE VAL PHE GLN TRP LEU PHE ASP GLU ALA
SEQRES 21 A 372 GLN MET ARG VAL ASP ASN VAL GLY ALA PRO VAL THR PRO
SEQRES 22 A 372 GLN GLN TRP ASN TYR ILE HIS GLU MET GLY GLY ALA LEU
SEQRES 23 A 372 ARG SER SER LEU ASP ASN VAL SER ALA VAL PHE ALA PRO
SEQRES 24 A 372 SER CYS ILE GLY HIS GLY VAL LEU PHE LYS ARG ASP TRP
SEQRES 25 A 372 VAL ASN ILE LYS ILE ASP ASP ILE SER LEU PRO SER ALA
SEQRES 26 A 372 LEU ARG CYS TRP GLU HIS SER THR ARG SER GLY ASN ASN
SEQRES 27 A 372 ASN GLY CYS GLY LEU ARG LEU LEU GLU ARG CYS SER TRP
SEQRES 28 A 372 PRO GLN CYS ASN HIS SER CYS PRO THR GLY THR HIS HIS
SEQRES 29 A 372 HIS HIS HIS HIS HIS HIS HIS HIS
SEQRES 1 B 372 GLU THR GLY ASP HIS ARG SER LEU LYS ARG ALA ASN LEU
SEQRES 2 B 372 ALA ASN THR SER ILE THR CYS ASN ASP GLY SER HIS ALA
SEQRES 3 B 372 GLY PHE TYR LEU ARG LYS HIS PRO SER SER LYS LYS TRP
SEQRES 4 B 372 ILE VAL LEU LEU GLU GLY GLY TRP HIS CYS PHE ASP VAL
SEQRES 5 B 372 ARG SER CYS ARG SER ARG TRP MET ARG LEU ARG HIS LEU
SEQRES 6 B 372 MET THR SER SER GLN TRP PRO GLU THR ARG ASP VAL GLY
SEQRES 7 B 372 GLY ILE LEU SER PRO HIS PRO GLU GLU ASN PRO TYR TRP
SEQRES 8 B 372 HIS ASN ALA ASN HIS VAL LEU ILE PRO TYR CYS SER SER
SEQRES 9 B 372 ASP SER TRP SER GLY THR ARG THR GLU PRO ASP THR SER
SEQRES 10 B 372 ASP ARG GLU ASN SER TRP ARG PHE MET GLY ALA LEU ILE
SEQRES 11 B 372 LEU ARG GLN VAL ILE ALA GLU LEU ILE PRO VAL GLY LEU
SEQRES 12 B 372 GLY ARG VAL PRO GLY GLY GLU LEU MET LEU VAL GLY SER
SEQRES 13 B 372 SER ALA GLY GLY MET GLY VAL MET LEU ASN LEU ASP ARG
SEQRES 14 B 372 ILE ARG ASP PHE LEU VAL ASN GLU LYS LYS LEU GLN ILE
SEQRES 15 B 372 THR VAL ARG GLY VAL SER ASP SER GLY TRP PHE LEU ASP
SEQRES 16 B 372 ARG GLU PRO TYR THR PRO ALA ALA VAL ALA SER ASN GLU
SEQRES 17 B 372 ALA VAL ARG GLN GLY TRP LYS LEU TRP GLN GLY LEU LEU
SEQRES 18 B 372 PRO GLU GLU CYS THR LYS SER TYR PRO THR GLU PRO TRP
SEQRES 19 B 372 ARG CYS TYR TYR GLY TYR ARG LEU TYR PRO THR LEU LYS
SEQRES 20 B 372 THR PRO LEU PHE VAL PHE GLN TRP LEU PHE ASP GLU ALA
SEQRES 21 B 372 GLN MET ARG VAL ASP ASN VAL GLY ALA PRO VAL THR PRO
SEQRES 22 B 372 GLN GLN TRP ASN TYR ILE HIS GLU MET GLY GLY ALA LEU
SEQRES 23 B 372 ARG SER SER LEU ASP ASN VAL SER ALA VAL PHE ALA PRO
SEQRES 24 B 372 SER CYS ILE GLY HIS GLY VAL LEU PHE LYS ARG ASP TRP
SEQRES 25 B 372 VAL ASN ILE LYS ILE ASP ASP ILE SER LEU PRO SER ALA
SEQRES 26 B 372 LEU ARG CYS TRP GLU HIS SER THR ARG SER GLY ASN ASN
SEQRES 27 B 372 ASN GLY CYS GLY LEU ARG LEU LEU GLU ARG CYS SER TRP
SEQRES 28 B 372 PRO GLN CYS ASN HIS SER CYS PRO THR GLY THR HIS HIS
SEQRES 29 B 372 HIS HIS HIS HIS HIS HIS HIS HIS
HET NAG B1617 14
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
FORMUL 3 NAG C8 H15 N O6
FORMUL 4 HOH *14(H2 O)
HELIX 1 1 ASP A 131 LEU A 142 1 12
HELIX 2 2 ARG A 143 MET A 146 5 4
HELIX 3 3 GLY A 158 SER A 162 5 5
HELIX 4 4 MET A 206 ILE A 219 1 14
HELIX 5 5 SER A 237 ASN A 256 1 20
HELIX 6 6 ALA A 285 GLN A 298 1 14
HELIX 7 7 PRO A 302 TYR A 309 1 8
HELIX 8 8 GLU A 312 TYR A 317 5 6
HELIX 9 9 TYR A 318 TYR A 323 1 6
HELIX 10 10 PRO A 324 LEU A 326 5 3
HELIX 11 11 GLU A 339 ASN A 346 1 8
HELIX 12 12 THR A 352 LEU A 370 1 19
HELIX 13 13 LYS A 389 ASN A 394 5 6
HELIX 14 14 LEU A 402 THR A 413 1 12
HELIX 15 15 ASP B 131 LEU B 142 1 12
HELIX 16 16 ARG B 143 MET B 146 5 4
HELIX 17 17 GLY B 158 SER B 162 5 5
HELIX 18 18 MET B 206 GLY B 222 1 17
HELIX 19 19 SER B 237 ASN B 256 1 20
HELIX 20 20 ALA B 285 GLN B 298 1 14
HELIX 21 21 PRO B 302 LYS B 307 1 6
HELIX 22 22 GLU B 312 TYR B 317 5 6
HELIX 23 23 TYR B 318 TYR B 323 1 6
HELIX 24 24 PRO B 324 LEU B 326 5 3
HELIX 25 25 GLU B 339 ASN B 346 1 8
HELIX 26 26 THR B 352 LEU B 370 1 19
HELIX 27 27 LYS B 389 ASN B 394 5 6
HELIX 28 28 LEU B 402 SER B 412 1 11
SHEET 1 AA10 THR A 154 ARG A 155 0
SHEET 2 AA10 LEU A 88 ASN A 92 -1 O LEU A 88 N ARG A 155
SHEET 3 AA10 GLY A 107 ARG A 111 -1 O PHE A 108 N ALA A 91
SHEET 4 AA10 ASN A 175 ILE A 179 -1 O HIS A 176 N ARG A 111
SHEET 5 AA10 LYS A 118 LEU A 123 1 O LYS A 118 N ASN A 175
SHEET 6 AA10 GLY A 229 SER A 236 1 O GLU A 230 N TRP A 119
SHEET 7 AA10 ILE A 262 ASP A 269 1 O THR A 263 N LEU A 231
SHEET 8 AA10 LEU A 330 PHE A 333 1 O PHE A 331 N SER A 268
SHEET 9 AA10 VAL A 376 ALA A 378 1 N PHE A 377 O VAL A 332
SHEET 10 AA10 ARG A 601 LEU A 603 1 O LEU A 602 N ALA A 378
SHEET 1 AB 2 PHE A 337 ASP A 338 0
SHEET 2 AB 2 ILE A 382 GLY A 383 1 N GLY A 383 O PHE A 337
SHEET 1 AC 2 LYS A 396 ILE A 397 0
SHEET 2 AC 2 ILE A 400 SER A 401 -1 O ILE A 400 N ILE A 397
SHEET 1 BA10 THR B 154 ARG B 155 0
SHEET 2 BA10 LEU B 88 ASN B 92 -1 O LEU B 88 N ARG B 155
SHEET 3 BA10 GLY B 107 ARG B 111 -1 O PHE B 108 N ALA B 91
SHEET 4 BA10 ASN B 175 ILE B 179 -1 O HIS B 176 N ARG B 111
SHEET 5 BA10 LYS B 118 LEU B 123 1 O LYS B 118 N ASN B 175
SHEET 6 BA10 GLY B 229 SER B 236 1 O GLU B 230 N TRP B 119
SHEET 7 BA10 ILE B 262 ASP B 269 1 O THR B 263 N LEU B 231
SHEET 8 BA10 LEU B 330 PHE B 333 1 O PHE B 331 N SER B 268
SHEET 9 BA10 VAL B 376 ALA B 378 1 N PHE B 377 O VAL B 332
SHEET 10 BA10 ARG B 601 LEU B 603 1 O LEU B 602 N ALA B 378
SHEET 1 BB 2 PHE B 337 ASP B 338 0
SHEET 2 BB 2 ILE B 382 GLY B 383 1 N GLY B 383 O PHE B 337
SHEET 1 BC 2 LYS B 396 ILE B 397 0
SHEET 2 BC 2 ILE B 400 SER B 401 -1 O ILE B 400 N ILE B 397
SSBOND 1 CYS A 100 CYS A 182 1555 1555 2.09
SSBOND 2 CYS A 129 CYS A 135 1555 1555 2.07
SSBOND 3 CYS A 305 CYS A 316 1555 1555 2.04
SSBOND 4 CYS A 381 CYS A 615 1555 1555 2.06
SSBOND 5 CYS A 606 CYS A 611 1555 1555 2.04
SSBOND 6 CYS B 100 CYS B 182 1555 1555 2.07
SSBOND 7 CYS B 129 CYS B 135 1555 1555 2.08
SSBOND 8 CYS B 305 CYS B 316 1555 1555 2.09
SSBOND 9 CYS B 381 CYS B 615 1555 1555 2.06
SSBOND 10 CYS B 606 CYS B 611 1555 1555 2.04
LINK ND2 ASN B 95 C1 NAG B1617 1555 1555 1.45
SITE 1 AC1 3 ASN B 95 SER B 97 ILE B 98
CRYST1 59.388 81.394 86.945 90.00 105.54 90.00 P 1 21 1 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.016838 0.000000 0.004682 0.00000
SCALE2 0.000000 0.012286 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011938 0.00000
MTRIX1 1 -1.000000 -0.010000 -0.011000 -25.59700
MTRIX2 1 0.002000 -0.829000 0.560000 -32.52700
MTRIX3 1 -0.015000 0.560000 0.829000 9.40500
TER 2736 THR A 617
TER 5471 PRO B 616
MASTER 452 0 1 28 28 0 1 9 5497 2 35 58
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