HEADER ISOMERASE/VIRAL PROTEIN 28-JUL-02 1M9D TITLE X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN TITLE 2 (1-146) O-TYPE CHIMERA COMPLEX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLOPHILIN A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A, PPIASE, ROTAMASE, COMPND 5 CYCLOSPORIN A-BINDING PROTEIN; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HIV-1 CAPSID; COMPND 10 CHAIN: C, D; COMPND 11 FRAGMENT: N-TERMINAL DOMAIN; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3A; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 12 ORGANISM_TAXID: 11676; SOURCE 13 GENE: CA; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS CAPSID, HIV-1, CYCLOPHILIN A, ISOMERASE, ROTAMASE, ISOMERASE-VIRAL KEYWDS 2 PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.R.HOWARD,F.F.VAJDOS,S.LI,W.I.SUNDQUIST,C.P.HILL REVDAT 4 14-FEB-24 1M9D 1 REMARK REVDAT 3 27-OCT-21 1M9D 1 SEQADV REVDAT 2 24-FEB-09 1M9D 1 VERSN REVDAT 1 27-MAY-03 1M9D 0 JRNL AUTH B.R.HOWARD,F.F.VAJDOS,S.LI,W.I.SUNDQUIST,C.P.HILL JRNL TITL STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM OF JRNL TITL 2 CYCLOPHILIN A JRNL REF NAT.STRUCT.BIOL. V. 10 475 2003 JRNL REFN ISSN 1072-8368 JRNL PMID 12730686 JRNL DOI 10.1038/NSB927 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : -3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 37052 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.500 REMARK 3 FREE R VALUE TEST SET COUNT : 3894 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2270 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.1830 REMARK 3 BIN FREE R VALUE SET COUNT : 186 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4779 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 584 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : 0.37000 REMARK 3 B33 (A**2) : -0.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.24000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.193 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.178 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.175 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.872 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4893 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4378 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6610 ; 2.922 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10251 ; 2.134 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 616 ; 5.758 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 913 ;19.590 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 707 ; 0.196 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5472 ; 0.019 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 958 ; 0.015 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1053 ; 0.206 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4520 ; 0.144 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1 ; 0.003 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 827 ; 0.190 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.032 ; 0.500 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): 22 ; 0.113 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 104 ; 0.137 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 63 ; 0.205 ; 0.500 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): 3072 ; 3.006 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4945 ; 4.317 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1821 ; 3.461 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1665 ; 5.125 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : BABINET MODEL WITH 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 BUT NOT OUTPUT TO THE COORDINATE FILE REMARK 4 REMARK 4 1M9D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016759. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(311) BENT REMARK 200 MONOCHROMATOR 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 : 37052 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 67.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.35200 REMARK 200 R SYM FOR SHELL (I) : 0.35200 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1AK4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8K, BICINE, LICL, TRIS, BETA REMARK 280 -MERCAPTOETHANOL, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 54.65000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC REMARK 300 UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 REMARK 300 FOR INFORMATION ON GENERATING THE BIOLOGICAL REMARK 300 MOLECULE(S). REMARK 300 COMPLEX "A" CONSISTS OF CHAINS B AND C; REMARK 300 COMPLEX "B" CONSISTS OF CHAINS A AND D. 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 APPLY THE FOLLOWING TO CHAINS: A, D 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 MET B 1 REMARK 465 VAL B 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU C 35 CG CD OE1 OE2 REMARK 470 GLU D 28 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 134 O HOH A 312 2.12 REMARK 500 O HOH C 229 O HOH C 271 2.17 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 PHE A 8 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ILE A 10 CG1 - CB - CG2 ANGL. DEV. = -15.3 DEGREES REMARK 500 ASP A 13 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 55 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 69 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 LYS A 118 CD - CE - NZ ANGL. DEV. = -15.7 DEGREES REMARK 500 LYS A 131 CD - CE - NZ ANGL. DEV. = 17.1 DEGREES REMARK 500 ARG B 37 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG B 55 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG B 69 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP B 123 CB - CG - OD2 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG B 144 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 148 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP B 160 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 VAL C 3 CA - CB - CG2 ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG C 18 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 MET C 39 CG - SD - CE ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG C 82 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG C 82 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG C 97 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG C 100 NE - CZ - NH1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG D 18 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 LEU D 20 CB - CG - CD2 ANGL. DEV. = 11.7 DEGREES REMARK 500 PHE D 40 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 LEU D 52 CB - CG - CD1 ANGL. DEV. = 18.6 DEGREES REMARK 500 LEU D 91 CB - CG - CD1 ANGL. DEV. = 14.3 DEGREES REMARK 500 ARG D 100 NE - CZ - NH1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG D 100 NE - CZ - NH2 ANGL. DEV. = -9.9 DEGREES REMARK 500 LEU D 111 CB - CG - CD1 ANGL. DEV. = 11.3 DEGREES REMARK 500 ARG D 143 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG D 143 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 TYR D 145 CB - CG - CD2 ANGL. DEV. = 4.1 DEGREES REMARK 500 TYR D 145 CD1 - CE1 - CZ ANGL. DEV. = 5.6 DEGREES REMARK 500 TYR D 145 OH - CZ - CE2 ANGL. DEV. = 19.7 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 PHE A 60 -79.27 -124.58 REMARK 500 HIS A 70 19.78 56.92 REMARK 500 GLU A 81 168.78 165.88 REMARK 500 LYS A 82 153.77 -41.74 REMARK 500 LYS A 133 -67.78 -104.46 REMARK 500 LEU A 164 -147.02 -114.47 REMARK 500 PHE B 60 -75.56 -128.98 REMARK 500 ASN B 71 13.76 -151.22 REMARK 500 LEU B 164 -131.88 -93.10 REMARK 500 ALA C 31 -84.61 3.99 REMARK 500 LEU D 6 -6.69 -58.07 REMARK 500 GLN D 9 136.69 63.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 PHE C 40 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ALA D 42 -12.75 REMARK 500 MET D 118 11.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AK4 RELATED DB: PDB REMARK 900 HUMAN CYCLOPHILIN A BOUND TO THE AMINO-TERMINAL DOMAIN OF HIV-1 REMARK 900 CAPSID (1-151) REMARK 900 RELATED ID: 1M96 RELATED DB: PDB REMARK 900 HIV-1 CA 1-146 A92E CRYSTAL STRUCTURE REMARK 900 RELATED ID: 1M9C RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN REMARK 900 (1-146) M-TYPE COMPLEX. REMARK 900 RELATED ID: 1M9E RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN REMARK 900 (1-146) M-TYPE COMPLEX. REMARK 900 RELATED ID: 1M9F RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN REMARK 900 (1-146) M-TYPE H87A,A88M COMPLEX. REMARK 900 RELATED ID: 1M9X RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN REMARK 900 (1-146) M-TYPE H87A,A88M,G89A COMPLEX. REMARK 900 RELATED ID: 1M9Y RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN REMARK 900 (1-146) M-TYPE H87A,G89A COMPLEX. REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO THE AUTHORS, THIS APPARENT CONFLICT IS REMARK 999 DUE TO THE USE OF HIV-1 STRAIN NL4-3 WHICH REMARK 999 HAS A HISTIDINE AT RESIDUE 120. DBREF 1M9D A 1 165 UNP P62937 PPIA_HUMAN 1 164 DBREF 1M9D B 1 165 UNP P62937 PPIA_HUMAN 1 164 DBREF 1M9D C 1 146 UNP Q72497 Q72497_9HIV1 133 278 DBREF 1M9D D 1 146 UNP Q72497 Q72497_9HIV1 133 278 SEQADV 1M9D THR C 83 UNP Q72497 LEU 215 ENGINEERED MUTATION SEQADV 1M9D PRO C 86 UNP Q72497 VAL 218 ENGINEERED MUTATION SEQADV 1M9D ALA C 87 UNP Q72497 HIS 219 ENGINEERED MUTATION SEQADV 1M9D MET C 88 UNP Q72497 ALA 220 ENGINEERED MUTATION SEQADV 1M9D LEU C 91 UNP Q72497 ILE 223 ENGINEERED MUTATION SEQADV 1M9D PRO C 92 UNP Q72497 ALA 224 ENGINEERED MUTATION SEQADV 1M9D ILE C 96 UNP Q72497 MET 228 ENGINEERED MUTATION SEQADV 1M9D HIS C 120 UNP Q72497 ASN 252 SEE REMARK 999 SEQADV 1M9D THR D 83 UNP Q72497 LEU 215 ENGINEERED MUTATION SEQADV 1M9D PRO D 86 UNP Q72497 VAL 218 ENGINEERED MUTATION SEQADV 1M9D ALA D 87 UNP Q72497 HIS 219 ENGINEERED MUTATION SEQADV 1M9D MET D 88 UNP Q72497 ALA 220 ENGINEERED MUTATION SEQADV 1M9D LEU D 91 UNP Q72497 ILE 223 ENGINEERED MUTATION SEQADV 1M9D PRO D 92 UNP Q72497 ALA 224 ENGINEERED MUTATION SEQADV 1M9D ILE D 96 UNP Q72497 MET 228 ENGINEERED MUTATION SEQADV 1M9D HIS D 120 UNP Q72497 ASN 252 SEE REMARK 999 SEQRES 1 A 165 MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL ASP SEQRES 2 A 165 GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE ALA SEQRES 3 A 165 ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU SEQRES 4 A 165 SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER CYS SEQRES 5 A 165 PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY GLY SEQRES 6 A 165 ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE SEQRES 7 A 165 TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU LYS SEQRES 8 A 165 HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA GLY SEQRES 9 A 165 PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ALA SEQRES 10 A 165 LYS THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY SEQRES 11 A 165 LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET GLU SEQRES 12 A 165 ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS ILE SEQRES 13 A 165 THR ILE ALA ASP CYS GLY GLN LEU GLU SEQRES 1 B 165 MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL ASP SEQRES 2 B 165 GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE ALA SEQRES 3 B 165 ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU SEQRES 4 B 165 SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER CYS SEQRES 5 B 165 PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY GLY SEQRES 6 B 165 ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE SEQRES 7 B 165 TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU LYS SEQRES 8 B 165 HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA GLY SEQRES 9 B 165 PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ALA SEQRES 10 B 165 LYS THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY SEQRES 11 B 165 LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET GLU SEQRES 12 B 165 ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS ILE SEQRES 13 B 165 THR ILE ALA ASP CYS GLY GLN LEU GLU SEQRES 1 C 146 PRO ILE VAL GLN ASN LEU GLN GLY GLN MET VAL HIS GLN SEQRES 2 C 146 ALA ILE SER PRO ARG THR LEU ASN ALA TRP VAL LYS VAL SEQRES 3 C 146 VAL GLU GLU LYS ALA PHE SER PRO GLU VAL ILE PRO MET SEQRES 4 C 146 PHE SER ALA LEU SER GLU GLY ALA THR PRO GLN ASP LEU SEQRES 5 C 146 ASN THR MET LEU ASN THR VAL GLY GLY HIS GLN ALA ALA SEQRES 6 C 146 MET GLN MET LEU LYS GLU THR ILE ASN GLU GLU ALA ALA SEQRES 7 C 146 GLU TRP ASP ARG THR HIS PRO PRO ALA MET GLY PRO LEU SEQRES 8 C 146 PRO PRO GLY GLN ILE ARG GLU PRO ARG GLY SER ASP ILE SEQRES 9 C 146 ALA GLY THR THR SER THR LEU GLN GLU GLN ILE GLY TRP SEQRES 10 C 146 MET THR HIS ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR SEQRES 11 C 146 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG SEQRES 12 C 146 MET TYR SER SEQRES 1 D 146 PRO ILE VAL GLN ASN LEU GLN GLY GLN MET VAL HIS GLN SEQRES 2 D 146 ALA ILE SER PRO ARG THR LEU ASN ALA TRP VAL LYS VAL SEQRES 3 D 146 VAL GLU GLU LYS ALA PHE SER PRO GLU VAL ILE PRO MET SEQRES 4 D 146 PHE SER ALA LEU SER GLU GLY ALA THR PRO GLN ASP LEU SEQRES 5 D 146 ASN THR MET LEU ASN THR VAL GLY GLY HIS GLN ALA ALA SEQRES 6 D 146 MET GLN MET LEU LYS GLU THR ILE ASN GLU GLU ALA ALA SEQRES 7 D 146 GLU TRP ASP ARG THR HIS PRO PRO ALA MET GLY PRO LEU SEQRES 8 D 146 PRO PRO GLY GLN ILE ARG GLU PRO ARG GLY SER ASP ILE SEQRES 9 D 146 ALA GLY THR THR SER THR LEU GLN GLU GLN ILE GLY TRP SEQRES 10 D 146 MET THR HIS ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR SEQRES 11 D 146 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG SEQRES 12 D 146 MET TYR SER FORMUL 5 HOH *584(H2 O) HELIX 1 1 VAL A 29 GLY A 42 1 14 HELIX 2 2 THR A 119 ASP A 123 5 5 HELIX 3 3 GLY A 135 ARG A 144 1 10 HELIX 4 4 VAL B 29 GLY B 42 1 14 HELIX 5 5 THR B 119 ASP B 123 5 5 HELIX 6 6 GLY B 135 ARG B 144 1 10 HELIX 7 7 SER C 16 ALA C 31 1 16 HELIX 8 8 GLU C 35 SER C 44 1 10 HELIX 9 9 THR C 48 THR C 58 1 11 HELIX 10 10 HIS C 62 HIS C 84 1 23 HELIX 11 11 ARG C 100 ALA C 105 1 6 HELIX 12 12 THR C 110 THR C 119 1 10 HELIX 13 13 PRO C 125 TYR C 145 1 21 HELIX 14 14 SER D 16 LYS D 30 1 15 HELIX 15 15 GLU D 35 LEU D 43 1 9 HELIX 16 16 THR D 48 THR D 58 1 11 HELIX 17 17 HIS D 62 HIS D 84 1 23 HELIX 18 18 ARG D 100 ALA D 105 1 6 HELIX 19 19 THR D 110 HIS D 120 1 11 HELIX 20 20 PRO D 125 SER D 146 1 22 SHEET 1 A 8 ARG A 55 ILE A 57 0 SHEET 2 A 8 MET A 61 GLY A 64 -1 O GLN A 63 N ARG A 55 SHEET 3 A 8 PHE A 112 CYS A 115 -1 O PHE A 112 N GLY A 64 SHEET 4 A 8 ILE A 97 MET A 100 -1 N SER A 99 O PHE A 113 SHEET 5 A 8 VAL A 128 VAL A 132 -1 O PHE A 129 N LEU A 98 SHEET 6 A 8 GLU A 15 LEU A 24 -1 N GLU A 23 O LYS A 131 SHEET 7 A 8 THR A 5 VAL A 12 -1 N ILE A 10 O LEU A 17 SHEET 8 A 8 ILE A 156 GLN A 163 -1 O ASP A 160 N ASP A 9 SHEET 1 B 8 PHE B 53 ILE B 57 0 SHEET 2 B 8 MET B 61 GLY B 64 -1 O GLN B 63 N ARG B 55 SHEET 3 B 8 PHE B 112 CYS B 115 -1 O ILE B 114 N CYS B 62 SHEET 4 B 8 ILE B 97 MET B 100 -1 N SER B 99 O PHE B 113 SHEET 5 B 8 VAL B 128 GLU B 134 -1 O PHE B 129 N LEU B 98 SHEET 6 B 8 GLU B 15 LEU B 24 -1 N SER B 21 O LYS B 133 SHEET 7 B 8 THR B 5 VAL B 12 -1 N PHE B 8 O VAL B 20 SHEET 8 B 8 ILE B 156 GLN B 163 -1 O ASP B 160 N ASP B 9 SHEET 1 C 2 ILE C 2 GLN C 4 0 SHEET 2 C 2 MET C 10 HIS C 12 -1 O VAL C 11 N VAL C 3 SHEET 1 D 2 ILE D 2 GLN D 4 0 SHEET 2 D 2 MET D 10 HIS D 12 -1 O VAL D 11 N VAL D 3 CISPEP 1 GLY C 89 PRO C 90 0 2.21 CISPEP 2 ASN C 121 PRO C 122 0 4.31 CISPEP 3 GLY D 89 PRO D 90 0 9.72 CISPEP 4 ASN D 121 PRO D 122 0 2.14 CRYST1 38.900 109.300 67.700 90.00 99.70 90.00 P 1 21 1 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 0.025707 0.000000 0.004394 0.00000 SCALE2 0.000000 0.009149 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014985 0.00000