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HEADER HYDROLASE 13-NOV-08 3F9C
TITLE CRYSTAL STRUCTURE OF HUMAN PLASMA PLATELET ACTIVATING FACTOR
TITLE 2 ACETYLHYDROLASE COVALENTLY INHIBITED BY
TITLE 3 DIISOPROPYLFLUOROPHOSPHATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: UNP RESIDUES 47-429;
COMPND 5 SYNONYM: PAF ACETYLHYDROLASE, PAF 2-ACYLHYDROLASE, LDL-
COMPND 6 ASSOCIATED PHOSPHOLIPASE A2, LDL-PLA(2), 2-ACETYL-1-
COMPND 7 ALKYLGLYCEROPHOSPHOCHOLINE ESTERASE, 1-ALKYL-2-
COMPND 8 ACETYLGLYCEROPHOSPHOCHOLINE ESTERASE;
COMPND 9 EC: 3.1.1.47;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: PLA2G7, PAFAH;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID
KEYWDS PLASMA PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE, SECRETED
KEYWDS 2 PROTEIN, ALPHA/BETA-HYDROLASE-FOLD, LDL-BOUND; LIPOPROTEIN
KEYWDS 3 ASSOCIATED PHOSPHOLIPASE A2, LP-PLA2, GROUP VIIA PLA2,
KEYWDS 4 GLYCOPROTEIN, HYDROLASE, LIPID DEGRADATION, POLYMORPHISM,
KEYWDS 5 DIISOPROPYLFLUOROPHOSPHATE, DFP, DISEASE MUTATION, SECRETED
EXPDTA X-RAY DIFFRACTION
AUTHOR U.SAMANTA,B.J.BAHNSON
REVDAT 1 23-JUN-09 3F9C 0
JRNL AUTH U.SAMANTA,S.D.KIRBY,P.SRINIVASAN,D.M.CERASOLI,
JRNL AUTH 2 B.J.BAHNSON
JRNL TITL CRYSTAL STRUCTURES OF HUMAN GROUP-VIIA
JRNL TITL 2 PHOSPHOLIPASE A2 INHIBITED BY ORGANOPHOSPHORUS
JRNL TITL 3 NERVE AGENTS EXHIBIT NON-AGED COMPLEXES.
JRNL REF BIOCHEM.PHARM. 2009
JRNL REFN ISSN 0006-2952
JRNL PMID 19394314
JRNL DOI 10.1016/J.BCP.2009.04.018
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
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) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 34789
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) : 0.199
REMARK 3 R VALUE (WORKING SET) : 0.196
REMARK 3 FREE R VALUE : 0.261
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1826
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) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2542
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78
REMARK 3 BIN R VALUE (WORKING SET) : 0.2450
REMARK 3 BIN FREE R VALUE SET COUNT : 121
REMARK 3 BIN FREE R VALUE : 0.3000
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5978
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 20
REMARK 3 SOLVENT ATOMS : 170
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.91
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.48000
REMARK 3 B22 (A**2) : 0.56000
REMARK 3 B33 (A**2) : 1.30000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.46000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.358
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.257
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.190
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.754
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6142 ; 0.020 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8301 ; 1.813 ; 1.953
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 739 ; 7.823 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 295 ;37.302 ;23.966
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1061 ;17.355 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;20.355 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 891 ; 0.119 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4654 ; 0.008 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2823 ; 0.231 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4082 ; 0.309 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 312 ; 0.167 ; 0.200
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): 54 ; 0.352 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.291 ; 0.200
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): 3816 ; 1.058 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5944 ; 1.752 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2693 ; 2.590 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2357 ; 3.825 ; 4.500
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 : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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 3F9C COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-08.
REMARK 100 THE RCSB ID CODE IS RCSB050309.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-MAY-08
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : OSMIC BLUE
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL2000
REMARK 200 DATA SCALING SOFTWARE : HKL2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36675
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 4.200
REMARK 200 R MERGE (I) : 0.06900
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 20.7100
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 4.10
REMARK 200 R MERGE FOR SHELL (I) : 0.44000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 3.230
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP OF CCP4I, REFMAC5 OF CCP4I FOR FINAL
REMARK 200 REFINEMENT
REMARK 200 STARTING MODEL: NATIVE STRUCTURE, PDB ENTRY 3D59
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.70
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.6. NATIVE PROTEIN CRYSTAL
REMARK 280 SOAKED IN MOTHER LIQUOR CONTAINING DFP, VAPOR DIFFUSION,
REMARK 280 HANGING DROP, TEMPERATURE 293.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 58.18750
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.20000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.18750
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 41.20000
REMARK 290 SMTRY3 4 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 ALA A 47
REMARK 465 ALA A 48
REMARK 465 ALA A 49
REMARK 465 SER A 50
REMARK 465 PHE A 51
REMARK 465 GLY A 52
REMARK 465 GLN A 53
REMARK 465 ASN A 426
REMARK 465 GLN A 427
REMARK 465 HIS A 428
REMARK 465 ILE A 429
REMARK 465 ALA B 47
REMARK 465 ALA B 48
REMARK 465 ALA B 49
REMARK 465 SER B 50
REMARK 465 PHE B 51
REMARK 465 GLY B 52
REMARK 465 GLN B 53
REMARK 465 GLN B 427
REMARK 465 HIS B 428
REMARK 465 ILE B 429
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 HIS A 272 C SER A 273 N 0.283
REMARK 500 SER A 273 C PHE A 274 N 0.283
REMARK 500 HIS B 272 C SER B 273 N 0.301
REMARK 500 SER B 273 C PHE B 274 N 0.299
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 ASP A 73 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 SER A 273 CA - C - N ANGL. DEV. = 23.3 DEGREES
REMARK 500 SER A 273 O - C - N ANGL. DEV. = -27.4 DEGREES
REMARK 500 SER B 273 CA - C - N ANGL. DEV. = 15.9 DEGREES
REMARK 500 SER B 273 O - C - N ANGL. DEV. = -20.4 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 ARG A 92 142.71 -171.51
REMARK 500 THR A 113 -148.23 -111.23
REMARK 500 PRO A 131 70.42 -68.88
REMARK 500 ALA A 155 -163.92 -101.60
REMARK 500 LYS A 266 75.42 -114.00
REMARK 500 SER A 273 -105.26 68.63
REMARK 500 SER A 336 134.49 -170.78
REMARK 500 HIS A 399 59.38 -118.54
REMARK 500 LYS A 400 -166.71 -121.25
REMARK 500 THR A 424 114.03 -32.35
REMARK 500 GLN B 88 -61.98 -90.58
REMARK 500 ASN B 90 88.31 -162.07
REMARK 500 THR B 113 -167.02 -107.98
REMARK 500 HIS B 114 -162.24 -109.04
REMARK 500 PRO B 131 65.83 -68.90
REMARK 500 LYS B 266 76.10 -106.74
REMARK 500 SER B 273 -108.16 79.58
REMARK 500 HIS B 399 64.66 -109.85
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 THR B 424 THR B 425 -130.93
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 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: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 ASN A 423 24.9 L L OUTSIDE RANGE
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 RESIDUE DFP A 473
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DFP B 473
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3D59 RELATED DB: PDB
REMARK 900 THE SAME WILD TYPE PROTEIN
REMARK 900 RELATED ID: 3D5E RELATED DB: PDB
REMARK 900 THE SAME PROTEIN COMPLEXED WITH PARAOXON
REMARK 900 RELATED ID: 3F96 RELATED DB: PDB
REMARK 900 THE SAME PROTEIN COMPLEXED WITH SARIN
REMARK 900 RELATED ID: 3F97 RELATED DB: PDB
REMARK 900 THE SAME PROTEIN COMPLEXED WITH SOMAN
REMARK 900 RELATED ID: 3F98 RELATED DB: PDB
REMARK 900 THE SAME PROTEIN COMPLEXED WITH TABUN
DBREF 3F9C A 47 429 UNP Q13093 PAFA_HUMAN 47 429
DBREF 3F9C B 47 429 UNP Q13093 PAFA_HUMAN 47 429
SEQRES 1 A 383 ALA ALA ALA SER PHE GLY GLN THR LYS ILE PRO ARG GLY
SEQRES 2 A 383 ASN GLY PRO TYR SER VAL GLY CYS THR ASP LEU MET PHE
SEQRES 3 A 383 ASP HIS THR ASN LYS GLY THR PHE LEU ARG LEU TYR TYR
SEQRES 4 A 383 PRO SER GLN ASP ASN ASP ARG LEU ASP THR LEU TRP ILE
SEQRES 5 A 383 PRO ASN LYS GLU TYR PHE TRP GLY LEU SER LYS PHE LEU
SEQRES 6 A 383 GLY THR HIS TRP LEU MET GLY ASN ILE LEU ARG LEU LEU
SEQRES 7 A 383 PHE GLY SER MET THR THR PRO ALA ASN TRP ASN SER PRO
SEQRES 8 A 383 LEU ARG PRO GLY GLU LYS TYR PRO LEU VAL VAL PHE SER
SEQRES 9 A 383 HIS GLY LEU GLY ALA PHE ARG THR LEU TYR SER ALA ILE
SEQRES 10 A 383 GLY ILE ASP LEU ALA SER HIS GLY PHE ILE VAL ALA ALA
SEQRES 11 A 383 VAL GLU HIS ARG ASP ARG SER ALA SER ALA THR TYR TYR
SEQRES 12 A 383 PHE LYS ASP GLN SER ALA ALA GLU ILE GLY ASP LYS SER
SEQRES 13 A 383 TRP LEU TYR LEU ARG THR LEU LYS GLN GLU GLU GLU THR
SEQRES 14 A 383 HIS ILE ARG ASN GLU GLN VAL ARG GLN ARG ALA LYS GLU
SEQRES 15 A 383 CYS SER GLN ALA LEU SER LEU ILE LEU ASP ILE ASP HIS
SEQRES 16 A 383 GLY LYS PRO VAL LYS ASN ALA LEU ASP LEU LYS PHE ASP
SEQRES 17 A 383 MET GLU GLN LEU LYS ASP SER ILE ASP ARG GLU LYS ILE
SEQRES 18 A 383 ALA VAL ILE GLY HIS SER PHE GLY GLY ALA THR VAL ILE
SEQRES 19 A 383 GLN THR LEU SER GLU ASP GLN ARG PHE ARG CYS GLY ILE
SEQRES 20 A 383 ALA LEU ASP ALA TRP MET PHE PRO LEU GLY ASP GLU VAL
SEQRES 21 A 383 TYR SER ARG ILE PRO GLN PRO LEU PHE PHE ILE ASN SER
SEQRES 22 A 383 GLU TYR PHE GLN TYR PRO ALA ASN ILE ILE LYS MET LYS
SEQRES 23 A 383 LYS CYS TYR SER PRO ASP LYS GLU ARG LYS MET ILE THR
SEQRES 24 A 383 ILE ARG GLY SER VAL HIS GLN ASN PHE ALA ASP PHE THR
SEQRES 25 A 383 PHE ALA THR GLY LYS ILE ILE GLY HIS MET LEU LYS LEU
SEQRES 26 A 383 LYS GLY ASP ILE ASP SER ASN VAL ALA ILE ASP LEU SER
SEQRES 27 A 383 ASN LYS ALA SER LEU ALA PHE LEU GLN LYS HIS LEU GLY
SEQRES 28 A 383 LEU HIS LYS ASP PHE ASP GLN TRP ASP CYS LEU ILE GLU
SEQRES 29 A 383 GLY ASP ASP GLU ASN LEU ILE PRO GLY THR ASN ILE ASN
SEQRES 30 A 383 THR THR ASN GLN HIS ILE
SEQRES 1 B 383 ALA ALA ALA SER PHE GLY GLN THR LYS ILE PRO ARG GLY
SEQRES 2 B 383 ASN GLY PRO TYR SER VAL GLY CYS THR ASP LEU MET PHE
SEQRES 3 B 383 ASP HIS THR ASN LYS GLY THR PHE LEU ARG LEU TYR TYR
SEQRES 4 B 383 PRO SER GLN ASP ASN ASP ARG LEU ASP THR LEU TRP ILE
SEQRES 5 B 383 PRO ASN LYS GLU TYR PHE TRP GLY LEU SER LYS PHE LEU
SEQRES 6 B 383 GLY THR HIS TRP LEU MET GLY ASN ILE LEU ARG LEU LEU
SEQRES 7 B 383 PHE GLY SER MET THR THR PRO ALA ASN TRP ASN SER PRO
SEQRES 8 B 383 LEU ARG PRO GLY GLU LYS TYR PRO LEU VAL VAL PHE SER
SEQRES 9 B 383 HIS GLY LEU GLY ALA PHE ARG THR LEU TYR SER ALA ILE
SEQRES 10 B 383 GLY ILE ASP LEU ALA SER HIS GLY PHE ILE VAL ALA ALA
SEQRES 11 B 383 VAL GLU HIS ARG ASP ARG SER ALA SER ALA THR TYR TYR
SEQRES 12 B 383 PHE LYS ASP GLN SER ALA ALA GLU ILE GLY ASP LYS SER
SEQRES 13 B 383 TRP LEU TYR LEU ARG THR LEU LYS GLN GLU GLU GLU THR
SEQRES 14 B 383 HIS ILE ARG ASN GLU GLN VAL ARG GLN ARG ALA LYS GLU
SEQRES 15 B 383 CYS SER GLN ALA LEU SER LEU ILE LEU ASP ILE ASP HIS
SEQRES 16 B 383 GLY LYS PRO VAL LYS ASN ALA LEU ASP LEU LYS PHE ASP
SEQRES 17 B 383 MET GLU GLN LEU LYS ASP SER ILE ASP ARG GLU LYS ILE
SEQRES 18 B 383 ALA VAL ILE GLY HIS SER PHE GLY GLY ALA THR VAL ILE
SEQRES 19 B 383 GLN THR LEU SER GLU ASP GLN ARG PHE ARG CYS GLY ILE
SEQRES 20 B 383 ALA LEU ASP ALA TRP MET PHE PRO LEU GLY ASP GLU VAL
SEQRES 21 B 383 TYR SER ARG ILE PRO GLN PRO LEU PHE PHE ILE ASN SER
SEQRES 22 B 383 GLU TYR PHE GLN TYR PRO ALA ASN ILE ILE LYS MET LYS
SEQRES 23 B 383 LYS CYS TYR SER PRO ASP LYS GLU ARG LYS MET ILE THR
SEQRES 24 B 383 ILE ARG GLY SER VAL HIS GLN ASN PHE ALA ASP PHE THR
SEQRES 25 B 383 PHE ALA THR GLY LYS ILE ILE GLY HIS MET LEU LYS LEU
SEQRES 26 B 383 LYS GLY ASP ILE ASP SER ASN VAL ALA ILE ASP LEU SER
SEQRES 27 B 383 ASN LYS ALA SER LEU ALA PHE LEU GLN LYS HIS LEU GLY
SEQRES 28 B 383 LEU HIS LYS ASP PHE ASP GLN TRP ASP CYS LEU ILE GLU
SEQRES 29 B 383 GLY ASP ASP GLU ASN LEU ILE PRO GLY THR ASN ILE ASN
SEQRES 30 B 383 THR THR ASN GLN HIS ILE
HET DFP A 473 10
HET DFP B 473 10
HETNAM DFP DIISOPROPYL PHOSPHONATE
FORMUL 3 DFP 2(C6 H15 O3 P)
FORMUL 5 HOH *170(H2 O)
HELIX 1 1 ASN A 100 LEU A 111 1 12
HELIX 2 2 HIS A 114 GLY A 126 1 13
HELIX 3 3 TYR A 160 SER A 169 1 10
HELIX 4 4 ASP A 192 GLY A 199 1 8
HELIX 5 5 LYS A 210 GLU A 212 5 3
HELIX 6 6 GLU A 213 HIS A 241 1 29
HELIX 7 7 ASP A 254 LYS A 259 5 6
HELIX 8 8 SER A 273 SER A 273 1 1
HELIX 9 9 PHE A 274 ASP A 286 1 13
HELIX 10 10 GLY A 303 ILE A 310 5 8
HELIX 11 11 TYR A 324 LYS A 333 1 10
HELIX 12 12 VAL A 350 ALA A 360 5 11
HELIX 13 13 GLY A 362 LYS A 370 1 9
HELIX 14 14 ASP A 376 GLY A 397 1 22
HELIX 15 15 ASP A 401 ILE A 409 5 9
HELIX 16 16 ASN B 100 GLY B 112 1 13
HELIX 17 17 HIS B 114 GLY B 126 1 13
HELIX 18 18 TYR B 160 HIS B 170 1 11
HELIX 19 19 ASP B 192 GLY B 199 1 8
HELIX 20 20 LYS B 210 GLU B 212 5 3
HELIX 21 21 GLU B 213 HIS B 241 1 29
HELIX 22 22 ASP B 254 LYS B 259 5 6
HELIX 23 23 SER B 273 SER B 273 1 1
HELIX 24 24 PHE B 274 ASP B 286 1 13
HELIX 25 25 GLU B 305 ARG B 309 5 5
HELIX 26 26 TYR B 324 LYS B 333 1 10
HELIX 27 27 VAL B 350 ALA B 360 5 11
HELIX 28 28 GLY B 362 LEU B 369 1 8
HELIX 29 29 ASP B 376 GLY B 397 1 22
HELIX 30 30 ASP B 401 GLN B 404 5 4
HELIX 31 31 TRP B 405 GLY B 411 1 7
SHEET 1 A10 ASN A 133 TRP A 134 0
SHEET 2 A10 SER A 64 PHE A 72 1 N VAL A 65 O ASN A 133
SHEET 3 A10 THR A 79 SER A 87 -1 O TYR A 85 N GLY A 66
SHEET 4 A10 ILE A 173 VAL A 177 -1 O ALA A 176 N ARG A 82
SHEET 5 A10 TYR A 144 SER A 150 1 N PHE A 149 O ALA A 175
SHEET 6 A10 ILE A 262 GLY A 271 1 O ILE A 270 N VAL A 148
SHEET 7 A10 CYS A 291 LEU A 295 1 O LEU A 295 N GLY A 271
SHEET 8 A10 LEU A 314 SER A 319 1 O PHE A 315 N ALA A 294
SHEET 9 A10 ARG A 341 ILE A 346 1 O LYS A 342 N PHE A 316
SHEET 10 A10 LEU A 416 PRO A 418 -1 O ILE A 417 N THR A 345
SHEET 1 B 2 THR A 95 LEU A 96 0
SHEET 2 B 2 THR A 129 THR A 130 -1 O THR A 130 N THR A 95
SHEET 1 C 2 ALA A 186 TYR A 189 0
SHEET 2 C 2 SER A 202 TYR A 205 -1 O SER A 202 N TYR A 189
SHEET 1 D10 ASN B 133 TRP B 134 0
SHEET 2 D10 SER B 64 PHE B 72 1 N VAL B 65 O ASN B 133
SHEET 3 D10 THR B 79 SER B 87 -1 O SER B 87 N SER B 64
SHEET 4 D10 ILE B 173 VAL B 177 -1 O VAL B 174 N TYR B 84
SHEET 5 D10 TYR B 144 SER B 150 1 N VAL B 147 O ALA B 175
SHEET 6 D10 ILE B 262 GLY B 271 1 O LYS B 266 N LEU B 146
SHEET 7 D10 CYS B 291 LEU B 295 1 O LEU B 295 N GLY B 271
SHEET 8 D10 LEU B 314 SER B 319 1 O ILE B 317 N ALA B 294
SHEET 9 D10 ARG B 341 ILE B 346 1 O ILE B 344 N ASN B 318
SHEET 10 D10 LEU B 416 PRO B 418 -1 O ILE B 417 N THR B 345
SHEET 1 E 2 THR B 95 LEU B 96 0
SHEET 2 E 2 THR B 129 THR B 130 -1 O THR B 130 N THR B 95
SHEET 1 F 2 ALA B 186 TYR B 189 0
SHEET 2 F 2 SER B 202 TYR B 205 -1 O SER B 202 N TYR B 189
LINK C HIS A 272 N SER A 273 1555 1555 1.62
LINK C SER A 273 N PHE A 274 1555 1555 1.62
LINK C HIS B 272 N SER B 273 1555 1555 1.64
LINK C SER B 273 N PHE B 274 1555 1555 1.64
LINK OG SER A 273 P DFP A 473 1555 1555 1.63
LINK OG SER B 273 P DFP B 473 1555 1555 1.62
CISPEP 1 PHE A 72 ASP A 73 0 -2.76
CISPEP 2 PHE B 72 ASP B 73 0 -5.91
SITE 1 AC1 7 GLY A 152 LEU A 153 HIS A 272 SER A 273
SITE 2 AC1 7 PHE A 274 HIS A 351 GLN A 352
SITE 1 AC2 6 GLY B 152 LEU B 153 SER B 273 PHE B 274
SITE 2 AC2 6 HIS B 351 GLN B 352
CRYST1 116.375 82.400 96.511 90.00 115.64 90.00 C 1 2 1 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 0.008593 0.000000 0.004125 0.00000
SCALE2 0.000000 0.012136 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011493 0.00000
TER 2986 THR A 425
TER 5980 ASN B 426
MASTER 398 0 2 31 28 0 4 6 6168 2 30 60
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