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HEADER HYDROLASE 05-SEP-14 4UZK
TITLE STRUCTURE OF THE WNT DEACYLASE NOTUM FROM DROSOPHILA -
TITLE 2 CRYSTAL FORM II - 1.9A
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: R416-K597 REPLACED BY GNNNG, 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 4UZK 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. 1.90 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) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 77.88
REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.56
REMARK 3 NUMBER OF REFLECTIONS : 61229
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) : 0.17677
REMARK 3 R VALUE (WORKING SET) : 0.17620
REMARK 3 FREE R VALUE : 0.20365
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.0
REMARK 3 FREE R VALUE TEST SET COUNT : 1252
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) : 1.900
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.949
REMARK 3 REFLECTION IN BIN (WORKING SET) : 4439
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.32
REMARK 3 BIN R VALUE (WORKING SET) : 0.248
REMARK 3 BIN FREE R VALUE SET COUNT : 106
REMARK 3 BIN FREE R VALUE : 0.265
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5640
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 28
REMARK 3 SOLVENT ATOMS : 219
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 31.7
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.866
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.44
REMARK 3 B22 (A**2) : 0.68
REMARK 3 B33 (A**2) : -0.24
REMARK 3 B12 (A**2) : 0.00
REMARK 3 B13 (A**2) : 0.00
REMARK 3 B23 (A**2) : 0.00
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.133
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.095
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.769
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5859 ; 0.015 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 5413 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7993 ; 1.594 ; 1.941
REMARK 3 BOND ANGLES OTHERS (DEGREES): 12429 ; 0.827 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 716 ; 6.166 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 270 ;34.109 ;22.222
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 942 ;13.546 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 58 ;16.452 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 837 ; 0.092 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6618 ; 0.008 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1456 ; 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): 2814 ; 2.288 ; 2.737
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2813 ; 2.286 ; 2.736
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3516 ; 3.374 ; 4.084
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3045 ; 3.277 ; 3.158
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 : A 2 A 617
REMARK 3 ORIGIN FOR THE GROUP (A): -27.8236 27.4737 -27.3630
REMARK 3 T TENSOR
REMARK 3 T11: 0.0315 T22: 0.0191
REMARK 3 T33: 0.0659 T12: 0.0225
REMARK 3 T13: 0.0023 T23: 0.0073
REMARK 3 L TENSOR
REMARK 3 L11: 0.3610 L22: 0.5139
REMARK 3 L33: 0.4528 L12: -0.1423
REMARK 3 L13: 0.1609 L23: -0.1795
REMARK 3 S TENSOR
REMARK 3 S11: 0.0206 S12: -0.0060 S13: -0.0581
REMARK 3 S21: -0.0432 S22: -0.0353 S23: -0.0735
REMARK 3 S31: -0.0766 S32: -0.0556 S33: 0.0147
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 : B 1 B 616
REMARK 3 ORIGIN FOR THE GROUP (A): -8.1103 -4.4647 -0.1736
REMARK 3 T TENSOR
REMARK 3 T11: 0.0445 T22: 0.0139
REMARK 3 T33: 0.0695 T12: -0.0107
REMARK 3 T13: -0.0210 T23: 0.0083
REMARK 3 L TENSOR
REMARK 3 L11: 0.4712 L22: 0.3915
REMARK 3 L33: 0.4891 L12: -0.1476
REMARK 3 L13: 0.1005 L23: -0.1622
REMARK 3 S TENSOR
REMARK 3 S11: -0.0099 S12: 0.0626 S13: 0.0212
REMARK 3 S21: 0.0431 S22: 0.0052 S23: -0.0116
REMARK 3 S31: 0.1022 S32: -0.0334 S33: 0.0047
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 4UZK 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-61705.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-APR-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 9.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I03
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PILATUS
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62554
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.90
REMARK 200 RESOLUTION RANGE LOW (A) : 142.00
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 6.5
REMARK 200 R MERGE (I) : 0.08
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 13.90
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 (%): 45
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.3
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NACL, 0.1 M LI2SO4, 0.1 M
REMARK 280 CAPSO PH 9.5, 12.0 %W/V PEG 4000
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-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 29.62600
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.06200
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.55150
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.06200
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.62600
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.55150
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2010 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 29540 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 9.4 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 80
REMARK 465 THR A 81
REMARK 465 GLY A 82
REMARK 465 ASP A 83
REMARK 465 HIS A 84
REMARK 465 SER A 85
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 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 80
REMARK 465 THR B 81
REMARK 465 GLY B 82
REMARK 465 ASP B 83
REMARK 465 HIS B 84
REMARK 465 SER B 85
REMARK 465 ASN B 418
REMARK 465 ASN B 419
REMARK 465 GLY B 420
REMARK 465 CYS B 598
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 ASP A 195 CG OD1 OD2
REMARK 470 THR A 196 OG1 CG2
REMARK 470 SER A 197 OG
REMARK 470 ASP A 198 CG OD1 OD2
REMARK 470 ARG A 199 CG CD NE CZ NH1 NH2
REMARK 470 ASP B 195 CG OD1 OD2
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 249 CG - CD - NE ANGL. DEV. = -13.2 DEGREES
REMARK 500 ARG A 249 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES
REMARK 500 ARG A 407 NE - CZ - NH2 ANGL. DEV. = -3.2 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 -148.59 65.45
REMARK 500 LEU A 142 48.78 -141.83
REMARK 500 SER A 237 -122.51 63.70
REMARK 500 PHE A 337 62.18 -112.84
REMARK 500 HIS A 384 113.62 -162.33
REMARK 500 VAL A 386 -28.01 -156.21
REMARK 500 TRP B 127 -147.25 64.29
REMARK 500 LEU B 142 53.48 -141.70
REMARK 500 ASP B 195 97.01 -60.07
REMARK 500 SER B 237 -122.62 62.66
REMARK 500 PHE B 337 61.55 -114.86
REMARK 500 VAL B 386 -30.67 -154.16
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 A1618 BOUND TO ASN A 95
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
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: 4UZJ RELATED DB: PDB
REMARK 900 STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM
REMARK 900 III - 1.4A
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 4UZK A 82 415 UNP Q9VUX3 Q9VUX3_DROME 82 415
DBREF 4UZK A 598 617 UNP Q9VUX3 Q9VUX3_DROME 598 617
DBREF 4UZK B 82 415 UNP Q9VUX3 Q9VUX3_DROME 82 415
DBREF 4UZK B 598 617 UNP Q9VUX3 Q9VUX3_DROME 598 617
SEQADV 4UZK GLU A 80 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK THR A 81 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK GLY A 416 UNP Q9VUX3 LINKER
SEQADV 4UZK ASN A 417 UNP Q9VUX3 LINKER
SEQADV 4UZK ASN A 418 UNP Q9VUX3 LINKER
SEQADV 4UZK ASN A 419 UNP Q9VUX3 LINKER
SEQADV 4UZK GLY A 420 UNP Q9VUX3 LINKER
SEQADV 4UZK GLY A 618 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK THR A 619 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS A 620 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS A 621 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS A 622 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS A 623 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS A 624 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS A 625 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS A 626 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS A 627 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS A 628 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS A 629 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK GLU B 80 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK THR B 81 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK GLY B 416 UNP Q9VUX3 LINKER
SEQADV 4UZK ASN B 417 UNP Q9VUX3 LINKER
SEQADV 4UZK ASN B 418 UNP Q9VUX3 LINKER
SEQADV 4UZK ASN B 419 UNP Q9VUX3 LINKER
SEQADV 4UZK GLY B 420 UNP Q9VUX3 LINKER
SEQADV 4UZK GLY B 618 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK THR B 619 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS B 620 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS B 621 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS B 622 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS B 623 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS B 624 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS B 625 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS B 626 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS B 627 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS B 628 UNP Q9VUX3 EXPRESSION TAG
SEQADV 4UZK HIS B 629 UNP Q9VUX3 EXPRESSION TAG
SEQRES 1 A 373 GLU THR GLY ASP HIS SER ARG SER LEU LYS ARG ALA ASN
SEQRES 2 A 373 LEU ALA ASN THR SER ILE THR CYS ASN ASP GLY SER HIS
SEQRES 3 A 373 ALA GLY PHE TYR LEU ARG LYS HIS PRO SER SER LYS LYS
SEQRES 4 A 373 TRP ILE VAL LEU LEU GLU GLY GLY TRP HIS CYS PHE ASP
SEQRES 5 A 373 VAL ARG SER CYS ARG SER ARG TRP MET ARG LEU ARG HIS
SEQRES 6 A 373 LEU MET THR SER SER GLN TRP PRO GLU THR ARG ASP VAL
SEQRES 7 A 373 GLY GLY ILE LEU SER PRO HIS PRO GLU GLU ASN PRO TYR
SEQRES 8 A 373 TRP HIS ASN ALA ASN HIS VAL LEU ILE PRO TYR CYS SER
SEQRES 9 A 373 SER ASP SER TRP SER GLY THR ARG THR GLU PRO ASP THR
SEQRES 10 A 373 SER ASP ARG GLU ASN SER TRP ARG PHE MET GLY ALA LEU
SEQRES 11 A 373 ILE LEU ARG GLN VAL ILE ALA GLU LEU ILE PRO VAL GLY
SEQRES 12 A 373 LEU GLY ARG VAL PRO GLY GLY GLU LEU MET LEU VAL GLY
SEQRES 13 A 373 SER SER ALA GLY GLY MET GLY VAL MET LEU ASN LEU ASP
SEQRES 14 A 373 ARG ILE ARG ASP PHE LEU VAL ASN GLU LYS LYS LEU GLN
SEQRES 15 A 373 ILE THR VAL ARG GLY VAL SER ASP SER GLY TRP PHE LEU
SEQRES 16 A 373 ASP ARG GLU PRO TYR THR PRO ALA ALA VAL ALA SER ASN
SEQRES 17 A 373 GLU ALA VAL ARG GLN GLY TRP LYS LEU TRP GLN GLY LEU
SEQRES 18 A 373 LEU PRO GLU GLU CYS THR LYS SER TYR PRO THR GLU PRO
SEQRES 19 A 373 TRP ARG CYS TYR TYR GLY TYR ARG LEU TYR PRO THR LEU
SEQRES 20 A 373 LYS THR PRO LEU PHE VAL PHE GLN TRP LEU PHE ASP GLU
SEQRES 21 A 373 ALA GLN MET ARG VAL ASP ASN VAL GLY ALA PRO VAL THR
SEQRES 22 A 373 PRO GLN GLN TRP ASN TYR ILE HIS GLU MET GLY GLY ALA
SEQRES 23 A 373 LEU ARG SER SER LEU ASP ASN VAL SER ALA VAL PHE ALA
SEQRES 24 A 373 PRO SER CYS ILE GLY HIS GLY VAL LEU PHE LYS ARG ASP
SEQRES 25 A 373 TRP VAL ASN ILE LYS ILE ASP ASP ILE SER LEU PRO SER
SEQRES 26 A 373 ALA LEU ARG CYS TRP GLU HIS SER THR ARG SER GLY ASN
SEQRES 27 A 373 ASN ASN GLY CYS GLY LEU ARG LEU LEU GLU ARG CYS SER
SEQRES 28 A 373 TRP PRO GLN CYS ASN HIS SER CYS PRO THR GLY THR HIS
SEQRES 29 A 373 HIS HIS HIS HIS HIS HIS HIS HIS HIS
SEQRES 1 B 373 GLU THR GLY ASP HIS SER ARG SER LEU LYS ARG ALA ASN
SEQRES 2 B 373 LEU ALA ASN THR SER ILE THR CYS ASN ASP GLY SER HIS
SEQRES 3 B 373 ALA GLY PHE TYR LEU ARG LYS HIS PRO SER SER LYS LYS
SEQRES 4 B 373 TRP ILE VAL LEU LEU GLU GLY GLY TRP HIS CYS PHE ASP
SEQRES 5 B 373 VAL ARG SER CYS ARG SER ARG TRP MET ARG LEU ARG HIS
SEQRES 6 B 373 LEU MET THR SER SER GLN TRP PRO GLU THR ARG ASP VAL
SEQRES 7 B 373 GLY GLY ILE LEU SER PRO HIS PRO GLU GLU ASN PRO TYR
SEQRES 8 B 373 TRP HIS ASN ALA ASN HIS VAL LEU ILE PRO TYR CYS SER
SEQRES 9 B 373 SER ASP SER TRP SER GLY THR ARG THR GLU PRO ASP THR
SEQRES 10 B 373 SER ASP ARG GLU ASN SER TRP ARG PHE MET GLY ALA LEU
SEQRES 11 B 373 ILE LEU ARG GLN VAL ILE ALA GLU LEU ILE PRO VAL GLY
SEQRES 12 B 373 LEU GLY ARG VAL PRO GLY GLY GLU LEU MET LEU VAL GLY
SEQRES 13 B 373 SER SER ALA GLY GLY MET GLY VAL MET LEU ASN LEU ASP
SEQRES 14 B 373 ARG ILE ARG ASP PHE LEU VAL ASN GLU LYS LYS LEU GLN
SEQRES 15 B 373 ILE THR VAL ARG GLY VAL SER ASP SER GLY TRP PHE LEU
SEQRES 16 B 373 ASP ARG GLU PRO TYR THR PRO ALA ALA VAL ALA SER ASN
SEQRES 17 B 373 GLU ALA VAL ARG GLN GLY TRP LYS LEU TRP GLN GLY LEU
SEQRES 18 B 373 LEU PRO GLU GLU CYS THR LYS SER TYR PRO THR GLU PRO
SEQRES 19 B 373 TRP ARG CYS TYR TYR GLY TYR ARG LEU TYR PRO THR LEU
SEQRES 20 B 373 LYS THR PRO LEU PHE VAL PHE GLN TRP LEU PHE ASP GLU
SEQRES 21 B 373 ALA GLN MET ARG VAL ASP ASN VAL GLY ALA PRO VAL THR
SEQRES 22 B 373 PRO GLN GLN TRP ASN TYR ILE HIS GLU MET GLY GLY ALA
SEQRES 23 B 373 LEU ARG SER SER LEU ASP ASN VAL SER ALA VAL PHE ALA
SEQRES 24 B 373 PRO SER CYS ILE GLY HIS GLY VAL LEU PHE LYS ARG ASP
SEQRES 25 B 373 TRP VAL ASN ILE LYS ILE ASP ASP ILE SER LEU PRO SER
SEQRES 26 B 373 ALA LEU ARG CYS TRP GLU HIS SER THR ARG SER GLY ASN
SEQRES 27 B 373 ASN ASN GLY CYS GLY LEU ARG LEU LEU GLU ARG CYS SER
SEQRES 28 B 373 TRP PRO GLN CYS ASN HIS SER CYS PRO THR GLY THR HIS
SEQRES 29 B 373 HIS HIS HIS HIS HIS HIS HIS HIS HIS
HET NAG A1618 14
HET NAG B1617 14
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
FORMUL 3 NAG 2(C8 H15 N O6)
FORMUL 4 HOH *219(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 PRO A 220 GLY A 222 5 3
HELIX 6 6 SER A 237 ASN A 256 1 20
HELIX 7 7 ALA A 285 GLN A 298 1 14
HELIX 8 8 PRO A 302 TYR A 309 1 8
HELIX 9 9 GLU A 312 TYR A 317 5 6
HELIX 10 10 TYR A 318 TYR A 323 1 6
HELIX 11 11 PRO A 324 LEU A 326 5 3
HELIX 12 12 GLU A 339 ASP A 345 1 7
HELIX 13 13 THR A 352 LEU A 370 1 19
HELIX 14 14 LYS A 389 ASN A 394 5 6
HELIX 15 15 LEU A 402 THR A 413 1 12
HELIX 16 16 ASP B 131 LEU B 142 1 12
HELIX 17 17 ARG B 143 MET B 146 5 4
HELIX 18 18 GLY B 158 SER B 162 5 5
HELIX 19 19 MET B 206 ILE B 219 1 14
HELIX 20 20 SER B 237 ASN B 256 1 20
HELIX 21 21 ALA B 285 GLN B 298 1 14
HELIX 22 22 PRO B 302 LYS B 307 1 6
HELIX 23 23 GLU B 312 TYR B 317 5 6
HELIX 24 24 TYR B 318 TYR B 323 1 6
HELIX 25 25 PRO B 324 LEU B 326 5 3
HELIX 26 26 GLU B 339 ASP B 345 1 7
HELIX 27 27 THR B 352 LEU B 370 1 19
HELIX 28 28 LYS B 389 ASN B 394 5 6
HELIX 29 29 LEU B 402 THR B 413 1 12
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 2.17
SSBOND 2 CYS A 129 CYS A 135 1555 1555 2.21
SSBOND 3 CYS A 305 CYS A 316 1555 1555 2.10
SSBOND 4 CYS A 381 CYS A 615 1555 1555 2.08
SSBOND 5 CYS A 408 CYS B 408 1555 1555 2.08
SSBOND 6 CYS A 606 CYS A 611 1555 1555 2.05
SSBOND 7 CYS B 100 CYS B 182 1555 1555 2.20
SSBOND 8 CYS B 129 CYS B 135 1555 1555 2.18
SSBOND 9 CYS B 305 CYS B 316 1555 1555 2.08
SSBOND 10 CYS B 381 CYS B 615 1555 1555 2.09
SSBOND 11 CYS B 606 CYS B 611 1555 1555 2.04
LINK ND2 ASN A 95 C1 NAG A1618 1555 1555 1.45
LINK ND2 ASN B 95 C1 NAG B1617 1555 1555 1.44
SITE 1 AC1 5 ASN A 95 SER A 97 ILE A 98 LEU A 209
SITE 2 AC1 5 HOH A2110
SITE 1 AC2 2 ASN B 95 ILE B 98
CRYST1 59.252 93.103 142.124 90.00 90.00 90.00 P 21 21 21 8
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 0.016877 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010741 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007036 0.00000
MTRIX1 1 -1.000000 0.010000 -0.009000 -35.83600 1
MTRIX2 1 -0.010000 -0.152000 0.988000 26.94600 1
MTRIX3 1 0.008000 0.988000 0.152000 -23.01900 1
TER 2808 THR A 617
TER 5642 PRO B 616
MASTER 438 0 2 29 28 0 3 9 5887 2 54 58
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