HEADER COMPLEX (ISOMERASE/PEPTIDE) 05-OCT-97 1AWU TITLE CYPA COMPLEXED WITH HVGPIA (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 MOL_ID: 2; COMPND 7 MOLECULE: PEPTIDE FROM THE HIV-1 CAPSID PROTEIN; COMPND 8 CHAIN: B; COMPND 9 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, PSEUDO- KEYWDS 2 SYMMETRY, COMPLEX (ISOMERASE-PEPTIDE) COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.F.VAJDOS REVDAT 4 22-MAY-24 1AWU 1 REMARK REVDAT 3 02-AUG-23 1AWU 1 REMARK REVDAT 2 24-FEB-09 1AWU 1 VERSN REVDAT 1 18-MAR-98 1AWU 0 JRNL AUTH F.F.VAJDOS,S.YOO,M.HOUSEWEART,W.I.SUNDQUIST,C.P.HILL JRNL TITL CRYSTAL STRUCTURE OF CYCLOPHILIN A COMPLEXED WITH A BINDING JRNL TITL 2 SITE PEPTIDE FROM THE HIV-1 CAPSID PROTEIN. JRNL REF PROTEIN SCI. V. 6 2297 1997 JRNL REFN ISSN 0961-8368 JRNL PMID 9385632 REMARK 2 REMARK 2 RESOLUTION. 2.34 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) : 2.34 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) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 7049 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) : 0.316 REMARK 3 FREE R VALUE : 0.351 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500 REMARK 3 FREE R VALUE TEST SET COUNT : 387 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.018 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) : 2.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.49 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 990 REMARK 3 BIN R VALUE (WORKING SET) : 0.4380 REMARK 3 BIN FREE R VALUE : 0.4690 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 59 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.061 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1300 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.60 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) : 0.45 REMARK 3 ESD FROM SIGMAA (A) : 0.55 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) : 0.58 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.70 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.350 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) : 5.580 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 7.790 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 7.550 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.760 ; 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 REMARK 3 REMARK 3 A LARGE NUMBER OF ATOMS WERE SET TO ZERO OCCUPANCY FOR REMARK 3 REFINEMENT PURPOSES SINCE THEY WERE NOT WELL-DEFINED BY THE REMARK 3 ELECTRON DENSITY. REMARK 3 REMARK 3 REGARDING THE HIGH R-VALUE: THIS IS THE STRUCTURE OF THE REMARK 3 COMPLEX REFINED IN A PSEUDO-SPACE GROUP. THE DETAILS ARE REMARK 3 ADDRESSED EXTENSIVELY IN THE PAPER. TO SUMMARIZE HERE, THE REMARK 3 HIGH R-VALUE FOR THIS STRUCTURE STEMS FROM THE BREAKDOWN IN REMARK 3 PSEUDO-SYMMETRY AT HIGH RESOLUTION. REMARK 4 REMARK 4 1AWU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171353. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-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 : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7251 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.340 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.11400 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.843 REMARK 200 STARTING MODEL: PDB ENTRY 2CYH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 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: 850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 VAL A 1002 REMARK 475 ASN A 1003 REMARK 475 ALA A 1026 REMARK 475 ASP A 1027 REMARK 475 LYS A 1028 REMARK 475 VAL A 1029 REMARK 475 PRO A 1030 REMARK 475 LYS A 1031 REMARK 475 GLY A 1042 REMARK 475 GLY A 1080 REMARK 475 GLU A 1081 REMARK 475 GLY A 1104 REMARK 475 PRO A 1105 REMARK 475 ARG A 1144 REMARK 475 LYS A 1154 REMARK 475 LYS A 1155 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 THR A 1032 CB OG1 CG2 REMARK 480 GLU A 1034 CB CG CD OE1 OE2 REMARK 480 LYS A 1049 CG CD CE NZ REMARK 480 ARG A 1069 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 1082 CB CG CD CE NZ REMARK 480 GLU A 1084 CB CG CD OE1 OE2 REMARK 480 ASP A 1085 CB CG OD1 OD2 REMARK 480 GLU A 1086 CB CG CD OE1 OE2 REMARK 480 ASN A 1087 CB CG OD1 ND2 REMARK 480 ASN A 1106 CG OD1 ND2 REMARK 480 LYS A 1131 CG CD CE NZ REMARK 480 GLU A 1134 CG CD OE1 OE2 REMARK 480 ASN A 1137 CG OD1 ND2 REMARK 480 ARG A 1148 CB CG CD NE CZ NH1 NH2 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 ASP A1013 65.75 69.55 REMARK 500 GLU A1015 97.67 -44.94 REMARK 500 LEU A1017 -69.54 -105.77 REMARK 500 ALA A1026 -76.61 -88.74 REMARK 500 GLU A1043 11.75 -62.18 REMARK 500 LYS A1044 25.98 -156.53 REMARK 500 THR A1068 -71.17 -84.84 REMARK 500 ASN A1071 -41.86 -161.85 REMARK 500 LYS A1076 143.09 174.39 REMARK 500 GLU A1081 -43.26 -143.06 REMARK 500 GLU A1084 164.86 -43.08 REMARK 500 HIS A1092 67.43 -69.09 REMARK 500 THR A1119 63.26 -113.48 REMARK 500 ARG A1144 -0.40 -59.59 REMARK 500 SER A1147 -173.25 -172.29 REMARK 500 LYS A1154 -109.23 -141.27 REMARK 500 LYS A1155 89.79 -167.53 REMARK 500 ASP A1160 169.21 178.43 REMARK 500 REMARK 500 REMARK: NULL DBREF 1AWU A 1002 1165 UNP P62937 PPIA_HUMAN 1 164 DBREF 1AWU B 1 6 PDB 1AWU 1AWU 1 6 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 MET 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 MET 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 MET ASN ILE VAL GLU ALA MET 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 VAL GLY PRO ILE ALA FORMUL 3 HOH *13(H2 O) HELIX 1 1 THR A 1032 THR A 1041 1 10 HELIX 2 2 GLU A 1120 LEU A 1122 5 3 HELIX 3 3 MET A 1136 PHE A 1145 1 10 SHEET 1 A 3 CYS A1161 GLN A1163 0 SHEET 2 A 3 THR A1005 ALA A1011 -1 N PHE A1007 O GLY A1162 SHEET 3 A 3 PRO A1016 GLU A1023 -1 N PHE A1022 O VAL A1006 SHEET 1 B 2 ILE A1010 VAL A1012 0 SHEET 2 B 2 ILE A1156 ILE A1158 -1 N THR A1157 O ALA A1011 SHEET 1 C 5 ARG A1055 ILE A1057 0 SHEET 2 C 5 MET A1061 GLY A1064 -1 N GLN A1063 O ARG A1055 SHEET 3 C 5 PHE A1112 CYS A1115 -1 N ILE A1114 O CYS A1062 SHEET 4 C 5 ILE A1097 MET A1100 -1 N SER A1099 O PHE A1113 SHEET 5 C 5 VAL A1128 LYS A1131 -1 N GLY A1130 O LEU A1098 CRYST1 52.400 52.400 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 0.019084 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019084 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015773 0.00000