HEADER ISOMERASE/VIRAL PROTEIN 28-JUL-02 1M9C TITLE X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN TITLE 2 (1-146) M-TYPE 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 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 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 3 14-FEB-24 1M9C 1 REMARK REVDAT 2 24-FEB-09 1M9C 1 VERSN REVDAT 1 27-MAY-03 1M9C 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : -3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.0 REMARK 3 NUMBER OF REFLECTIONS : 28437 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3125 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1575 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 169 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4712 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 144 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.95000 REMARK 3 B22 (A**2) : 3.71000 REMARK 3 B33 (A**2) : -1.91000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.40000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.315 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.236 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.252 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.916 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4797 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4285 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6474 ; 2.704 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10017 ; 1.634 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 604 ; 5.066 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 881 ;19.120 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 690 ; 0.162 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5376 ; 0.015 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 954 ; 0.007 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1044 ; 0.219 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4469 ; 0.162 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1 ; 0.031 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 543 ; 0.173 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 4 ; 0.027 ; 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): 19 ; 0.184 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 67 ; 0.162 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.256 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): 1 ; 0.141 ; 0.500 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): 3008 ; 2.687 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4830 ; 3.824 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1789 ; 2.723 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1644 ; 3.860 ; 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 1M9C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016758. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31588 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.0 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : 0.06300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.55 REMARK 200 R MERGE FOR SHELL (I) : 0.19500 REMARK 200 R SYM FOR SHELL (I) : 0.19500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 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): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8K, BICINE, LICL, TRIS, BETA REMARK 280 -MERCAPTOETHANOL, PH 8.0, 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 56.61750 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 465 PRO D 1 REMARK 465 ILE D 2 REMARK 465 VAL D 3 REMARK 465 GLN D 4 REMARK 465 ASN D 5 REMARK 465 LEU D 6 REMARK 465 GLN D 7 REMARK 465 GLY D 8 REMARK 465 GLN D 9 REMARK 465 MET D 10 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 ALA D 31 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 GLN C 4 CB CG CD OE1 NE2 REMARK 480 LYS C 25 CB CG CD CE NZ REMARK 480 GLN C 112 CB CG CD OE1 NE2 REMARK 480 GLU D 28 CB 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 NZ LYS B 31 OE2 GLU B 84 2.01 REMARK 500 O LYS D 30 N PHE D 32 2.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLN C 4 CA GLN C 4 CB -0.185 REMARK 500 GLN C 112 CA GLN C 112 CB 0.252 REMARK 500 GLU D 28 CA GLU D 28 CB -0.322 REMARK 500 LYS D 30 C ALA D 31 N 0.289 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 ASP A 9 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 19 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 55 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 66 CB - CG - OD2 ANGL. DEV. = 8.2 DEGREES REMARK 500 ASP A 85 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 GLU A 120 OE1 - CD - OE2 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 144 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ASP B 9 CB - CG - OD2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ASP B 13 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP B 27 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG B 69 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP B 85 CB - CG - OD2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ASP C 51 CB - CG - OD2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG C 82 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG C 100 NE - CZ - NH1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG C 100 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP C 103 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 GLN C 112 N - CA - CB ANGL. DEV. = -14.7 DEGREES REMARK 500 MET C 118 CG - SD - CE ANGL. DEV. = -9.9 DEGREES REMARK 500 GLU D 28 N - CA - CB ANGL. DEV. = 13.8 DEGREES REMARK 500 LYS D 30 CA - C - N ANGL. DEV. = -21.3 DEGREES REMARK 500 LYS D 30 O - C - N ANGL. DEV. = -41.1 DEGREES REMARK 500 MET D 66 CG - SD - CE ANGL. DEV. = -10.3 DEGREES REMARK 500 ASP D 81 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG D 100 NE - CZ - NH1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG D 100 NE - CZ - NH2 ANGL. DEV. = -5.1 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 PHE A 60 -74.25 -127.58 REMARK 500 ASN A 71 -13.92 -142.77 REMARK 500 PHE B 60 -76.37 -129.10 REMARK 500 GLU B 81 -57.29 -127.65 REMARK 500 ASN B 102 -166.02 -106.67 REMARK 500 PHE B 129 -2.77 -140.87 REMARK 500 GLN C 7 9.63 -64.66 REMARK 500 ALA C 31 -129.32 60.29 REMARK 500 HIS D 120 152.13 -47.56 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 LYS D 30 -35.35 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: 1M9D RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/HIV-1 CA N-TERMINAL DOMAIN REMARK 900 (1-146) O-TYPE CHIMERA 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 1M9C A 1 165 UNP P62937 PPIA_HUMAN 1 164 DBREF 1M9C B 1 165 UNP P62937 PPIA_HUMAN 1 164 DBREF 1M9C C 1 146 UNP Q72497 Q72497_9HIV1 133 278 DBREF 1M9C D 1 146 UNP Q72497 Q72497_9HIV1 133 278 SEQADV 1M9C HIS C 120 UNP Q72497 ASN 252 SEE REMARK 999 SEQADV 1M9C 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 LEU HIS PRO VAL HIS ALA GLY PRO ILE SEQRES 8 C 146 ALA PRO GLY GLN MET 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 LEU HIS PRO VAL HIS ALA GLY PRO ILE SEQRES 8 D 146 ALA PRO GLY GLN MET 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 *144(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 ASN C 57 1 10 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 HIS C 120 1 11 HELIX 13 13 PRO C 125 ARG C 143 1 19 HELIX 14 14 SER D 16 LYS D 30 1 15 HELIX 15 15 GLU D 35 SER D 44 1 10 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 9 CYS A 52 PHE A 53 0 SHEET 2 A 9 ILE A 156 LEU A 164 -1 O ILE A 156 N PHE A 53 SHEET 3 A 9 THR A 5 VAL A 12 -1 N ASP A 9 O ASP A 160 SHEET 4 A 9 GLU A 15 LEU A 24 -1 O LEU A 17 N ILE A 10 SHEET 5 A 9 VAL A 128 GLU A 134 -1 O LYS A 133 N SER A 21 SHEET 6 A 9 ILE A 97 MET A 100 -1 N LEU A 98 O PHE A 129 SHEET 7 A 9 PHE A 112 CYS A 115 -1 O PHE A 113 N SER A 99 SHEET 8 A 9 MET A 61 GLY A 64 -1 N CYS A 62 O ILE A 114 SHEET 9 A 9 ARG A 55 ILE A 57 -1 N ARG A 55 O GLN A 63 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 GLY B 130 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 VAL B 12 O GLU B 15 SHEET 8 B 8 ILE B 156 GLU B 165 -1 O LEU B 164 N THR B 5 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 CISPEP 1 ASN C 121 PRO C 122 0 -3.10 CISPEP 2 ASN D 121 PRO D 122 0 0.82 CRYST1 38.445 113.235 67.006 90.00 100.53 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 0.026011 0.000000 0.004833 0.00000 SCALE2 0.000000 0.008831 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015179 0.00000