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HEADER HYDROLASE 27-JUL-17 5OLJ
TITLE CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS DIPEPTIDYL PEPTIDASE 4
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DIPEPTIDYL PEPTIDASE IV;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS;
SOURCE 3 ORGANISM_TAXID: 837;
SOURCE 4 GENE: DPPIV, PGN_1469;
SOURCE 5 EXPRESSION_SYSTEM: PORPHYROMONAS GINGIVALIS;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 837
KEYWDS DIPEPTIDYL PEPTIDASE 4, PEPTIDASE INHIBITOR, PORPHYROMONAS
KEYWDS 2 GINGIVALIS, BIOFILM, DIPEPTIDYL PEPTIDASE 9, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR V.FULOP
REVDAT 1 06-SEP-17 5OLJ 0
JRNL AUTH D.REA,R.VAN ELZEN,H.DE WINTER,S.VAN GOETHEM,B.LANDUYT,
JRNL AUTH 2 W.LUYTEN,L.SCHOOFS,P.VAN DER VEKEN,K.AUGUSTYNS,I.DE MEESTER,
JRNL AUTH 3 V.FULOP,A.M.LAMBEIR
JRNL TITL CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS DIPEPTIDYL
JRNL TITL 2 PEPTIDASE 4 AND STRUCTURE-ACTIVITY RELATIONSHIPS BASED ON
JRNL TITL 3 INHIBITOR PROFILING.
JRNL REF EUR J MED CHEM V. 139 482 2017
JRNL REFN ISSN 1768-3254
JRNL PMID 28826083
JRNL DOI 10.1016/J.EJMECH.2017.08.024
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH D.REA,A.M.LAMBEIR,Y.KUMAGAI,I.DE MEESTER,S.SCHARPE,V.FULOP
REMARK 1 TITL EXPRESSION, PURIFICATION AND PRELIMINARY CRYSTALLOGRAPHIC
REMARK 1 TITL 2 ANALYSIS OF DIPEPTIDYL PEPTIDASE IV FROM PORPHYROMONAS
REMARK 1 TITL 3 GINGIVALIS.
REMARK 1 REF ACTA CRYSTALLOGR. D BIOL. V. 60 1871 2004
REMARK 1 REF 2 CRYSTALLOGR.
REMARK 1 REFN ISSN 0907-4449
REMARK 1 PMID 15388936
REMARK 1 DOI 10.1107/S0907444904017639
REMARK 2
REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.7.0029
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.87
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 46837
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) : 0.225
REMARK 3 R VALUE (WORKING SET) : 0.224
REMARK 3 FREE R VALUE : 0.255
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1974
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) : 2.20
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3288
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.61
REMARK 3 BIN R VALUE (WORKING SET) : 0.5290
REMARK 3 BIN FREE R VALUE SET COUNT : 137
REMARK 3 BIN FREE R VALUE : 0.5310
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5631
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 6
REMARK 3 SOLVENT ATOMS : 398
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.43
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.75000
REMARK 3 B22 (A**2) : -0.75000
REMARK 3 B33 (A**2) : 1.50000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.258
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.204
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.784
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.839
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.810
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5774 ; 0.014 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 5334 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7826 ; 1.634 ; 1.942
REMARK 3 BOND ANGLES OTHERS (DEGREES): 12236 ; 0.812 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 702 ; 7.154 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 284 ;33.536 ;23.380
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 948 ;16.061 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;21.102 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 834 ; 0.094 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6608 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1422 ; 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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER 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 : 4
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 21 A 43
REMARK 3 ORIGIN FOR THE GROUP (A): 49.6962 37.1992 16.0372
REMARK 3 T TENSOR
REMARK 3 T11: 0.0749 T22: 0.1115
REMARK 3 T33: 0.0090 T12: -0.0342
REMARK 3 T13: 0.0210 T23: -0.0210
REMARK 3 L TENSOR
REMARK 3 L11: 9.1110 L22: 3.0108
REMARK 3 L33: 3.7690 L12: -3.5623
REMARK 3 L13: 2.8972 L23: -1.8613
REMARK 3 S TENSOR
REMARK 3 S11: 0.1437 S12: 0.6439 S13: -0.0122
REMARK 3 S21: -0.0539 S22: -0.0832 S23: 0.0101
REMARK 3 S31: -0.3074 S32: 0.2134 S33: -0.0604
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 44 A 80
REMARK 3 ORIGIN FOR THE GROUP (A): 25.1933 43.3797 2.3556
REMARK 3 T TENSOR
REMARK 3 T11: 0.0539 T22: 0.0457
REMARK 3 T33: 0.0175 T12: -0.0309
REMARK 3 T13: -0.0163 T23: 0.0064
REMARK 3 L TENSOR
REMARK 3 L11: 1.4082 L22: 4.4739
REMARK 3 L33: 1.3677 L12: 1.9872
REMARK 3 L13: -0.8439 L23: 0.0065
REMARK 3 S TENSOR
REMARK 3 S11: 0.0798 S12: -0.0116 S13: -0.0667
REMARK 3 S21: -0.0004 S22: -0.0781 S23: -0.1508
REMARK 3 S31: -0.1127 S32: -0.0493 S33: -0.0017
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 81 A 321
REMARK 3 ORIGIN FOR THE GROUP (A): 19.2924 58.1134 22.9238
REMARK 3 T TENSOR
REMARK 3 T11: 0.0532 T22: 0.0368
REMARK 3 T33: 0.0282 T12: 0.0094
REMARK 3 T13: -0.0135 T23: -0.0125
REMARK 3 L TENSOR
REMARK 3 L11: 0.2653 L22: 0.2512
REMARK 3 L33: 0.3427 L12: 0.1042
REMARK 3 L13: 0.0076 L23: -0.0449
REMARK 3 S TENSOR
REMARK 3 S11: -0.0330 S12: -0.0023 S13: 0.0395
REMARK 3 S21: -0.0361 S22: -0.0018 S23: 0.0503
REMARK 3 S31: -0.0395 S32: -0.0624 S33: 0.0348
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 322 A 723
REMARK 3 ORIGIN FOR THE GROUP (A): 36.3683 35.0938 32.7516
REMARK 3 T TENSOR
REMARK 3 T11: 0.0625 T22: 0.0304
REMARK 3 T33: 0.0095 T12: -0.0004
REMARK 3 T13: -0.0173 T23: -0.0098
REMARK 3 L TENSOR
REMARK 3 L11: 0.2874 L22: 0.2356
REMARK 3 L33: 0.2898 L12: 0.1178
REMARK 3 L13: 0.1027 L23: 0.0851
REMARK 3 S TENSOR
REMARK 3 S11: 0.0101 S12: 0.0131 S13: -0.0157
REMARK 3 S21: 0.0322 S22: 0.0085 S23: -0.0034
REMARK 3 S31: 0.0413 S32: 0.0066 S33: -0.0186
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 RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 5OLJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JUL-17.
REMARK 100 THE DEPOSITION ID IS D_1200006012.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 09-JUL-11
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : SEALED TUBE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : XENOCS GENIX 3D CU HF
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48811
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 38.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 9.300
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 10.8000
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: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: 5KBY
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 57.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (W/V) PEG 8000, 20% (V/V) ETHYLENE
REMARK 280 GLYCOL, 0.02 M SODIUM L-GLUTAMATE, 0.02 M DL-ALANINE, 0.02 M
REMARK 280 GLYCINE, 0.02 M DL-LYSINE, 0.02 M DLSERINE, AND 0.1 M BICINE/
REMARK 280 TRIS PH 8.5, VAPOR DIFFUSION, TEMPERATURE 290K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
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 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.90500
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 54.55000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 54.55000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.45250
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 54.55000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 54.55000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 118.35750
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 54.55000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.55000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.45250
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 54.55000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.55000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 118.35750
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 78.90500
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 300 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 28330 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL
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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A1101 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A1170 LIES ON A SPECIAL POSITION.
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 MET A 1
REMARK 465 LYS A 2
REMARK 465 ARG A 3
REMARK 465 PRO A 4
REMARK 465 VAL A 5
REMARK 465 ILE A 6
REMARK 465 ILE A 7
REMARK 465 LEU A 8
REMARK 465 LEU A 9
REMARK 465 LEU A 10
REMARK 465 GLY A 11
REMARK 465 ILE A 12
REMARK 465 VAL A 13
REMARK 465 THR A 14
REMARK 465 MET A 15
REMARK 465 CYS A 16
REMARK 465 ALA A 17
REMARK 465 MET A 18
REMARK 465 ALA A 19
REMARK 465 GLN A 20
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 NZ LYS A 376 O HOH A 901 2.08
REMARK 500 SD MET A 559 O HOH A 1252 2.15
REMARK 500 OD2 ASP A 238 O HOH A 902 2.19
REMARK 500
REMARK 500 REMARK: NULL
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 83 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 ARG A 83 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES
REMARK 500 MET A 227 CG - SD - CE ANGL. DEV. = -11.0 DEGREES
REMARK 500 ARG A 280 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 ASP A 499 CB - CG - OD2 ANGL. DEV. = -5.5 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 SER A 40 -165.77 -122.48
REMARK 500 ARG A 43 83.74 -57.73
REMARK 500 ILE A 113 -74.07 -102.53
REMARK 500 TYR A 114 -154.05 -122.60
REMARK 500 ASN A 182 19.80 54.88
REMARK 500 SER A 183 -67.38 -145.95
REMARK 500 ARG A 324 -64.61 -107.78
REMARK 500 THR A 478 -170.34 -170.33
REMARK 500 ALA A 485 43.75 73.77
REMARK 500 ASP A 497 59.11 -101.39
REMARK 500 SER A 512 -5.12 81.71
REMARK 500 GLN A 560 51.91 -155.35
REMARK 500 SER A 593 -123.13 70.61
REMARK 500 ALA A 617 52.73 37.35
REMARK 500 ARG A 635 -167.92 56.64
REMARK 500 ASN A 640 49.91 -147.60
REMARK 500 ASN A 670 -65.42 -103.68
REMARK 500 ASP A 697 19.93 56.53
REMARK 500 ILE A 702 76.57 33.50
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 ARG A 43 GLY A 44 141.12
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A1298 DISTANCE = 7.01 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 801
DBREF 5OLJ A 1 723 UNP B2RKU3 B2RKU3_PORG3 1 723
SEQRES 1 A 723 MET LYS ARG PRO VAL ILE ILE LEU LEU LEU GLY ILE VAL
SEQRES 2 A 723 THR MET CYS ALA MET ALA GLN THR GLY ASP LYS PRO VAL
SEQRES 3 A 723 ASP LEU LYS GLU ILE THR SER GLY MET PHE TYR ALA ARG
SEQRES 4 A 723 SER ALA GLY ARG GLY ILE ARG SER MET PRO ASP GLY GLU
SEQRES 5 A 723 HIS TYR THR GLU MET ASN ARG GLU ARG THR ALA ILE VAL
SEQRES 6 A 723 ARG TYR ASN TYR ALA SER GLY LYS ALA VAL ASP THR LEU
SEQRES 7 A 723 PHE SER ILE GLU ARG ALA ARG GLU CYS PRO PHE LYS GLN
SEQRES 8 A 723 ILE GLN ASN TYR GLU VAL SER SER THR GLY HIS HIS ILE
SEQRES 9 A 723 LEU LEU PHE THR ASP MET GLU SER ILE TYR ARG HIS SER
SEQRES 10 A 723 TYR ARG ALA ALA VAL TYR ASP TYR ASP VAL ARG ARG ASN
SEQRES 11 A 723 LEU VAL LYS PRO LEU SER GLU HIS VAL GLY LYS VAL MET
SEQRES 12 A 723 ILE PRO THR PHE SER PRO ASP GLY ARG MET VAL ALA PHE
SEQRES 13 A 723 VAL ARG ASP ASN ASN ILE PHE ILE LYS LYS PHE ASP PHE
SEQRES 14 A 723 ASP THR GLU VAL GLN VAL THR THR ASP GLY GLN ILE ASN
SEQRES 15 A 723 SER VAL LEU ASN GLY ALA THR ASP TRP VAL TYR GLU GLU
SEQRES 16 A 723 GLU PHE GLY VAL THR ASN LEU MET SER TRP SER ALA ASP
SEQRES 17 A 723 ASN ALA PHE LEU ALA PHE VAL ARG SER ASP GLU SER ALA
SEQRES 18 A 723 VAL PRO GLU TYR ARG MET PRO MET TYR GLU ASP LYS LEU
SEQRES 19 A 723 TYR PRO GLU ASP TYR THR TYR LYS TYR PRO LYS ALA GLY
SEQRES 20 A 723 GLU LYS ASN SER THR VAL SER LEU HIS LEU TYR ASN VAL
SEQRES 21 A 723 ALA ASP ARG ASN THR LYS SER VAL SER LEU PRO ILE ASP
SEQRES 22 A 723 ALA ASP GLY TYR ILE PRO ARG ILE ALA PHE THR ASP ASN
SEQRES 23 A 723 ALA ASP GLU LEU ALA VAL MET THR LEU ASN ARG LEU GLN
SEQRES 24 A 723 ASN ASP PHE LYS MET TYR TYR VAL HIS PRO LYS SER LEU
SEQRES 25 A 723 VAL PRO LYS LEU ILE LEU GLN ASP MET ASN LYS ARG TYR
SEQRES 26 A 723 VAL ASP SER ASP TRP ILE GLN ALA LEU LYS PHE THR ALA
SEQRES 27 A 723 GLY GLY GLY PHE ALA TYR VAL SER GLU LYS ASP GLY PHE
SEQRES 28 A 723 ALA HIS ILE TYR LEU TYR ASP ASN LYS GLY VAL MET HIS
SEQRES 29 A 723 ARG ARG ILE THR SER GLY ASN TRP ASP VAL THR LYS LEU
SEQRES 30 A 723 TYR GLY VAL ASP ALA SER GLY THR VAL PHE TYR GLN SER
SEQRES 31 A 723 ALA GLU GLU SER PRO ILE ARG ARG ALA VAL TYR ALA ILE
SEQRES 32 A 723 ASP ALA LYS GLY ARG LYS THR LYS LEU SER LEU ASN VAL
SEQRES 33 A 723 GLY THR ASN ASP ALA LEU PHE SER GLY ASN TYR ALA TYR
SEQRES 34 A 723 TYR ILE ASN THR TYR SER SER ALA ALA THR PRO THR VAL
SEQRES 35 A 723 VAL SER VAL PHE ARG SER LYS GLY ALA LYS GLU LEU ARG
SEQRES 36 A 723 THR LEU GLU ASP ASN VAL ALA LEU ARG GLU ARG LEU LYS
SEQRES 37 A 723 ALA TYR ARG TYR ASN PRO LYS GLU PHE THR ILE ILE LYS
SEQRES 38 A 723 THR GLN SER ALA LEU GLU LEU ASN ALA TRP ILE VAL LYS
SEQRES 39 A 723 PRO ILE ASP PHE ASP PRO SER ARG HIS TYR PRO VAL LEU
SEQRES 40 A 723 MET VAL GLN TYR SER GLY PRO ASN SER GLN GLN VAL LEU
SEQRES 41 A 723 ASP ARG TYR SER PHE ASP TRP GLU HIS TYR LEU ALA SER
SEQRES 42 A 723 LYS GLY TYR VAL VAL ALA CYS VAL ASP GLY ARG GLY THR
SEQRES 43 A 723 GLY ALA ARG GLY GLU GLU TRP ARG LYS CYS THR TYR MET
SEQRES 44 A 723 GLN LEU GLY VAL PHE GLU SER ASP ASP GLN ILE ALA ALA
SEQRES 45 A 723 ALA THR ALA ILE GLY GLN LEU PRO TYR VAL ASP ALA ALA
SEQRES 46 A 723 ARG ILE GLY ILE TRP GLY TRP SER TYR GLY GLY TYR THR
SEQRES 47 A 723 THR LEU MET SER LEU CYS ARG GLY ASN GLY THR PHE LYS
SEQRES 48 A 723 ALA GLY ILE ALA VAL ALA PRO VAL ALA ASP TRP ARG PHE
SEQRES 49 A 723 TYR ASP SER VAL TYR THR GLU ARG PHE MET ARG THR PRO
SEQRES 50 A 723 LYS GLU ASN ALA SER GLY TYR LYS MET SER SER ALA LEU
SEQRES 51 A 723 ASP VAL ALA SER GLN LEU GLN GLY ASN LEU LEU ILE VAL
SEQRES 52 A 723 SER GLY SER ALA ASP ASP ASN VAL HIS LEU GLN ASN THR
SEQRES 53 A 723 MET LEU PHE THR GLU ALA LEU VAL GLN ALA ASN ILE PRO
SEQRES 54 A 723 PHE ASP MET ALA ILE TYR MET ASP LYS ASN HIS SER ILE
SEQRES 55 A 723 TYR GLY GLY ASN THR ARG TYR HIS LEU TYR THR ARG LYS
SEQRES 56 A 723 ALA LYS PHE LEU PHE ASP ASN LEU
HET GOL A 801 6
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 GOL C3 H8 O3
FORMUL 3 HOH *398(H2 O)
HELIX 1 AA1 ASP A 27 SER A 33 1 7
HELIX 2 AA2 ASP A 190 GLY A 198 1 9
HELIX 3 AA3 ASP A 327 ALA A 333 1 7
HELIX 4 AA4 ASN A 460 TYR A 470 1 11
HELIX 5 AA5 TRP A 527 SER A 533 1 7
HELIX 6 AA6 GLY A 550 CYS A 556 1 7
HELIX 7 AA7 GLY A 562 GLY A 577 1 16
HELIX 8 AA8 SER A 593 GLY A 606 1 14
HELIX 9 AA9 ASP A 621 TYR A 625 5 5
HELIX 10 AB1 ASP A 626 ARG A 635 1 10
HELIX 11 AB2 ASN A 640 SER A 647 1 8
HELIX 12 AB3 ALA A 649 LEU A 656 5 8
HELIX 13 AB4 HIS A 672 ALA A 686 1 15
HELIX 14 AB5 ASN A 706 LEU A 723 1 18
SHEET 1 AA1 4 ARG A 46 SER A 47 0
SHEET 2 AA1 4 HIS A 53 MET A 57 -1 O THR A 55 N ARG A 46
SHEET 3 AA1 4 ALA A 63 ASN A 68 -1 O TYR A 67 N TYR A 54
SHEET 4 AA1 4 ALA A 74 SER A 80 -1 O ASP A 76 N ARG A 66
SHEET 1 AA2 4 ASN A 94 VAL A 97 0
SHEET 2 AA2 4 HIS A 103 SER A 112 -1 O PHE A 107 N ASN A 94
SHEET 3 AA2 4 TYR A 118 ASP A 126 -1 O TYR A 123 N LEU A 106
SHEET 4 AA2 4 LEU A 131 PRO A 134 -1 O LEU A 131 N ASP A 126
SHEET 1 AA3 4 MET A 143 PHE A 147 0
SHEET 2 AA3 4 MET A 153 ARG A 158 -1 O ALA A 155 N THR A 146
SHEET 3 AA3 4 ASN A 161 LYS A 166 -1 O LYS A 165 N VAL A 154
SHEET 4 AA3 4 THR A 171 GLN A 174 -1 O THR A 171 N LYS A 166
SHEET 1 AA4 3 VAL A 184 ASN A 186 0
SHEET 2 AA4 3 PHE A 211 ASP A 218 -1 O SER A 217 N LEU A 185
SHEET 3 AA4 3 MET A 203 TRP A 205 -1 N SER A 204 O ALA A 213
SHEET 1 AA5 4 VAL A 184 ASN A 186 0
SHEET 2 AA5 4 PHE A 211 ASP A 218 -1 O SER A 217 N LEU A 185
SHEET 3 AA5 4 THR A 252 ASN A 259 -1 O SER A 254 N ARG A 216
SHEET 4 AA5 4 ASN A 264 VAL A 268 -1 O VAL A 268 N LEU A 255
SHEET 1 AA6 2 GLU A 224 MET A 229 0
SHEET 2 AA6 2 GLU A 237 LYS A 242 -1 O TYR A 239 N MET A 227
SHEET 1 AA7 4 TYR A 277 PHE A 283 0
SHEET 2 AA7 4 LEU A 290 LEU A 295 -1 O LEU A 295 N TYR A 277
SHEET 3 AA7 4 ASP A 301 VAL A 307 -1 O TYR A 305 N VAL A 292
SHEET 4 AA7 4 PRO A 314 MET A 321 -1 O ILE A 317 N MET A 304
SHEET 1 AA8 4 LYS A 335 PHE A 336 0
SHEET 2 AA8 4 PHE A 342 SER A 346 -1 O ALA A 343 N LYS A 335
SHEET 3 AA8 4 HIS A 353 TYR A 357 -1 O TYR A 355 N TYR A 344
SHEET 4 AA8 4 MET A 363 ARG A 366 -1 O ARG A 365 N LEU A 356
SHEET 1 AA9 4 VAL A 374 VAL A 380 0
SHEET 2 AA9 4 VAL A 386 SER A 390 -1 O PHE A 387 N GLY A 379
SHEET 3 AA9 4 ALA A 399 ILE A 403 -1 O TYR A 401 N TYR A 388
SHEET 4 AA9 4 LYS A 409 LYS A 411 -1 O THR A 410 N ALA A 402
SHEET 1 AB1 4 THR A 418 PHE A 423 0
SHEET 2 AB1 4 TYR A 429 SER A 435 -1 O THR A 433 N ASP A 420
SHEET 3 AB1 4 VAL A 442 ARG A 447 -1 O PHE A 446 N TYR A 430
SHEET 4 AB1 4 LYS A 452 GLU A 458 -1 O LEU A 454 N VAL A 445
SHEET 1 AB2 8 GLU A 476 LYS A 481 0
SHEET 2 AB2 8 GLU A 487 VAL A 493 -1 O ILE A 492 N GLU A 476
SHEET 3 AB2 8 VAL A 537 VAL A 541 -1 O VAL A 538 N VAL A 493
SHEET 4 AB2 8 TYR A 504 VAL A 509 1 N PRO A 505 O VAL A 537
SHEET 5 AB2 8 VAL A 582 TRP A 592 1 O ASP A 583 N TYR A 504
SHEET 6 AB2 8 ALA A 612 VAL A 616 1 O VAL A 616 N GLY A 591
SHEET 7 AB2 8 ASN A 659 GLY A 665 1 O ASN A 659 N GLY A 613
SHEET 8 AB2 8 ASP A 691 TYR A 695 1 O ASP A 691 N LEU A 660
SITE 1 AC1 4 TYR A 511 SER A 593 TYR A 594 TYR A 625
CRYST1 109.100 109.100 157.810 90.00 90.00 90.00 P 41 21 2 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 0.009166 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009166 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006337 0.00000
TER 5632 LEU A 723
MASTER 476 0 1 14 45 0 1 6 6035 1 6 56
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