HEADER COMPLEX (ISOMERASE/PEPTIDE) 04-OCT-97 1AWQ TITLE CYPA 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 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 3 02-AUG-23 1AWQ 1 REMARK REVDAT 2 24-FEB-09 1AWQ 1 VERSN REVDAT 1 18-MAR-98 1AWQ 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. 1.58 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) : 1.58 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) (%) : 88.3 REMARK 3 NUMBER OF REFLECTIONS : 19855 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) : 0.343 REMARK 3 FREE R VALUE : 0.433 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 960 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.014 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) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.68 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 59.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2096 REMARK 3 BIN R VALUE (WORKING SET) : 0.5690 REMARK 3 BIN FREE R VALUE : 0.5110 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 103 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1298 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 52 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.20 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) : 0.59 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) : 0.54 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.66 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.200 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) : 2.890 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.280 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.740 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.760 ; 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 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 1AWQ 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_1000171349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-95 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) : 1.100 REMARK 200 MONOCHROMATOR : SI(111) 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 : 24895 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 88.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08600 REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.15600 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2CYH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 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 31.40000 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 47.10000 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 15.70000 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: 790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7290 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: 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 PRO A1030 C - N - CA ANGL. DEV. = 10.1 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 VAL A1029 79.79 -117.47 REMARK 500 GLU A1043 9.17 -56.28 REMARK 500 PHE A1046 -102.66 -105.61 REMARK 500 PHE A1060 -78.75 -119.80 REMARK 500 ASN A1071 -30.89 -132.10 REMARK 500 SER A1077 -158.33 -75.77 REMARK 500 TYR A1079 60.05 -108.15 REMARK 500 GLU A1081 -78.15 -126.08 REMARK 500 ASN A1087 -176.25 175.74 REMARK 500 SER A1147 -165.83 -166.48 REMARK 500 REMARK 500 REMARK: NULL DBREF 1AWQ A 1002 1165 UNP P62937 PPIA_HUMAN 1 164 DBREF 1AWQ B 1 6 PDB 1AWQ 1AWQ 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 ALA GLY PRO ILE ALA 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 MET A 1136 GLU A 1143 1 8 SHEET 1 A 8 ARG A1055 ILE A1057 0 SHEET 2 A 8 MET 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 MET 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 CRYST1 51.500 51.500 62.800 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 0.019417 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019417 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015924 0.00000