HEADER COMPLEX (ISOMERASE/PEPTIDE) 04-OCT-97 1AWS
TITLE SECYPA COMPLEXED WITH HAGPIA (PSEUDO-SYMMETRIC MONOMER)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CYCLOPHILIN A;
COMPND 3 CHAIN: A;
COMPND 4 EC: 5.2.1.8;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN;
COMPND 9 CHAIN: B;
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 CELLULAR_LOCATION: CYTOPLASM;
SOURCE 6 GENE: CYCLOPHILIN;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 9 EXPRESSION_SYSTEM_GENE: CYCLOPHILIN;
SOURCE 10 MOL_ID: 2
KEYWDS COMPLEX (ISOMERASE/PEPTIDE), CYCLOPHILIN A, HIV-1 CAPSID,
KEYWDS 2 PSEUDO-SYMMETRY
EXPDTA X-RAY DIFFRACTION
AUTHOR F.F.VAJDOS
REVDAT 2 24-FEB-09 1AWS 1 VERSN
REVDAT 1 18-MAR-98 1AWS 0
JRNL AUTH F.F.VAJDOS,S.YOO,M.HOUSEWEART,W.I.SUNDQUIST,
JRNL AUTH 2 C.P.HILL
JRNL TITL CRYSTAL STRUCTURE OF CYCLOPHILIN A COMPLEXED WITH
JRNL TITL 2 A BINDING SITE PEPTIDE FROM THE HIV-1 CAPSID
JRNL TITL 3 PROTEIN.
JRNL REF PROTEIN SCI. V. 6 2297 1997
JRNL REFN ISSN 0961-8368
JRNL PMID 9385632
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 2.55 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.843
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2
REMARK 3 NUMBER OF REFLECTIONS : 5484
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 SET) : 0.262
REMARK 3 FREE R VALUE : 0.337
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500
REMARK 3 FREE R VALUE TEST SET COUNT : 304
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.019
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.55
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.71
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.10
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 871
REMARK 3 BIN R VALUE (WORKING SET) : 0.3810
REMARK 3 BIN FREE R VALUE : 0.5060
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.60
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 42
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.078
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1258
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 40
REMARK 3 SOLVENT ATOMS : 52
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 16.80
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.50
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.37
REMARK 3 ESD FROM SIGMAA (A) : 0.50
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.48
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.72
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.50
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.90
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.30
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 4.370 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.950 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 5.560 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.900 ; 2.500
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO
REMARK 3 PARAMETER FILE 2 : TIP3P.PARAMETER
REMARK 3 PARAMETER FILE 3 : NULL
REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO
REMARK 3 TOPOLOGY FILE 2 : TIP3P.TOPOLOGY
REMARK 3 TOPOLOGY FILE 3 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED THE PROTEIN
REMARK 3 IS SELENO-METHIONINE SUBSTITUTED, BUT THE SELENO-METHIONINE
REMARK 3 RESIDUES WERE REFINED AS METHIONINES. REGARDING THE HIGH R-
REMARK 3 VALUE: THIS IS THE STRUCTURE OF THE COMPLEX REFINED IN A
REMARK 3 PSEUDO-SPACE GROUP. THE DETAILS ARE ADDRESSED EXTENSIVELY IN
REMARK 3 THE PAPER. TO SUMMARIZE HERE, THE HIGH R-VALUE FOR THIS
REMARK 3 STRUCTURE STEMS FROM THE BREAKDOWN IN PSEUDO-SYMMETRY AT HIGH
REMARK 3 RESOLUTION.
REMARK 4
REMARK 4 1AWS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : JUN-96
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X12C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE AREA DETECTOR
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5576
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550
REMARK 200 RESOLUTION RANGE LOW (A) : 15.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.03500
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.07900
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: X-PLOR 3.843
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.22
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.4
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43
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,X,Z+3/4
REMARK 290 4555 Y,-X,Z+1/4
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 31.70000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.55000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 15.85000
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: 740 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 7490 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 VAL A1029 70.82 -113.20
REMARK 500 PRO A1030 -76.44 -51.84
REMARK 500 GLU A1043 7.05 -47.54
REMARK 500 LYS A1044 -4.07 -150.96
REMARK 500 PHE A1046 -86.09 -100.62
REMARK 500 ASN A1071 -34.47 -134.86
REMARK 500 TYR A1079 37.54 -93.09
REMARK 500 GLU A1081 -63.00 -140.34
REMARK 500 ASN A1087 -176.81 -174.98
REMARK 500 HIS A1092 69.95 -59.25
REMARK 500 PRO A1105 139.76 -28.76
REMARK 500 ALA A1117 161.96 174.37
REMARK 500 PHE A1129 -1.21 -147.98
REMARK 500 SER A1147 -152.62 -154.23
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 A 233 DISTANCE = 5.75 ANGSTROMS
REMARK 525 HOH A 238 DISTANCE = 7.32 ANGSTROMS
REMARK 525 HOH A 243 DISTANCE = 7.37 ANGSTROMS
REMARK 525 HOH A 252 DISTANCE = 6.87 ANGSTROMS
DBREF 1AWS A 1002 1165 UNP P62937 PPIA_HUMAN 1 164
DBREF 1AWS B 1 6 PDB 1AWS 1AWS 1 6
SEQADV 1AWS MSE A 1061 UNP P62937 MET 60 MODIFIED RESIDUE
SEQADV 1AWS MSE A 1100 UNP P62937 MET 99 MODIFIED RESIDUE
SEQADV 1AWS MSE A 1136 UNP P62937 MET 135 MODIFIED RESIDUE
SEQADV 1AWS MSE A 1142 UNP P62937 MET 141 MODIFIED RESIDUE
SEQRES 1 A 164 VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL ASP GLY
SEQRES 2 A 164 GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE ALA ASP
SEQRES 3 A 164 LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU SER
SEQRES 4 A 164 THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER CYS PHE
SEQRES 5 A 164 HIS ARG ILE ILE PRO GLY PHE MSE CYS GLN GLY GLY ASP
SEQRES 6 A 164 PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE TYR
SEQRES 7 A 164 GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU LYS HIS
SEQRES 8 A 164 THR GLY PRO GLY ILE LEU SER MSE ALA ASN ALA GLY PRO
SEQRES 9 A 164 ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ALA LYS
SEQRES 10 A 164 THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY LYS
SEQRES 11 A 164 VAL LYS GLU GLY MSE ASN ILE VAL GLU ALA MSE GLU ARG
SEQRES 12 A 164 PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS ILE THR
SEQRES 13 A 164 ILE ALA ASP CYS GLY GLN LEU GLU
SEQRES 1 B 6 HIS ALA GLY PRO ILE ALA
MODRES 1AWS MSE A 1061 MET SELENOMETHIONINE
MODRES 1AWS MSE A 1100 MET SELENOMETHIONINE
MODRES 1AWS MSE A 1136 MET SELENOMETHIONINE
MODRES 1AWS MSE A 1142 MET SELENOMETHIONINE
HET MSE A1061 8
HET MSE A1100 8
HET MSE A1136 8
HET MSE A1142 8
HETNAM MSE SELENOMETHIONINE
FORMUL 1 MSE 4(C5 H11 N O2 SE)
FORMUL 3 HOH *52(H2 O)
HELIX 1 1 PRO A 1030 THR A 1041 1 12
HELIX 2 2 GLU A 1120 LEU A 1122 5 3
HELIX 3 3 MSE A 1136 ARG A 1144 1 9
SHEET 1 A 8 ARG A1055 ILE A1057 0
SHEET 2 A 8 MSE A1061 GLY A1064 -1 N GLN A1063 O ARG A1055
SHEET 3 A 8 PHE A1112 CYS A1115 -1 N ILE A1114 O CYS A1062
SHEET 4 A 8 ILE A1097 MSE A1100 -1 N SER A1099 O PHE A1113
SHEET 5 A 8 VAL A1128 GLU A1134 -1 N GLY A1130 O LEU A1098
SHEET 6 A 8 GLU A1015 LEU A1024 -1 N GLU A1023 O LYS A1131
SHEET 7 A 8 THR A1005 VAL A1012 -1 N VAL A1012 O GLU A1015
SHEET 8 A 8 ILE A1156 GLN A1163 -1 N GLY A1162 O PHE A1007
LINK N MSE A1061 C PHE A1060 1555 1555 1.34
LINK C MSE A1061 N CYS A1062 1555 1555 1.34
LINK N MSE A1100 C SER A1099 1555 1555 1.32
LINK C MSE A1100 N ALA A1101 1555 1555 1.33
LINK N MSE A1136 C GLY A1135 1555 1555 1.33
LINK C MSE A1136 N ASN A1137 1555 1555 1.33
LINK N MSE A1142 C ALA A1141 1555 1555 1.34
LINK C MSE A1142 N GLU A1143 1555 1555 1.33
CRYST1 51.900 51.900 63.400 90.00 90.00 90.00 P 43 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 0.019268 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019268 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015773 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
