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 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 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