HEADER ISOMERASE/ISOMERASE INHIBITOR 17-JUN-96 1LOP TITLE CYCLOPHILIN A COMPLEXED WITH SUCCINYL-ALA-PRO-ALA-P-NITROANILIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLOPHILIN A; COMPND 3 CHAIN: A; COMPND 4 EC: 5.2.1.8; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SUCCINYL-ALA-PRO-ALA-P-NITROANILIDE; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES KEYWDS ROTAMASE, ISOMERASE-ISOMERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.KONNO REVDAT 5 29-NOV-17 1LOP 1 HELIX REVDAT 4 13-JUL-11 1LOP 1 VERSN REVDAT 3 25-AUG-09 1LOP 1 SOURCE REVDAT 2 24-FEB-09 1LOP 1 VERSN REVDAT 1 23-DEC-96 1LOP 0 JRNL AUTH M.KONNO,M.ITO,T.HAYANO,N.TAKAHASHI JRNL TITL THE SUBSTRATE-BINDING SITE IN ESCHERICHIA COLI CYCLOPHILIN A JRNL TITL 2 PREFERABLY RECOGNIZES A CIS-PROLINE ISOMER OR A HIGHLY JRNL TITL 3 DISTORTED FORM OF THE TRANS ISOMER. JRNL REF J.MOL.BIOL. V. 256 897 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 8601841 JRNL DOI 10.1006/JMBI.1996.0136 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 79.0 REMARK 3 NUMBER OF REFLECTIONS : 12783 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1312 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.00 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) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 2.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LOP 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_1000174783. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 288 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : WEIS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13690 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIPLE ISOMORPHOUS REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 33.16500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.01500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.11500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.01500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.16500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.11500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE SUCCINYL-ALA-PRO-ALA-P-NITROANILIDE IS PEPTIDE-LIKE, A MEMBER REMARK 400 OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: SUCCINYL-ALA-PRO-ALA-P-NITROANILIDE REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: 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 HIS A 5 NE2 HIS A 5 CD2 -0.069 REMARK 500 HIS A 8 NE2 HIS A 8 CD2 -0.067 REMARK 500 HIS A 42 NE2 HIS A 42 CD2 -0.072 REMARK 500 HIS A 92 NE2 HIS A 92 CD2 -0.070 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 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 32 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 80 CG - CD - NE ANGL. DEV. = -14.8 DEGREES REMARK 500 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG A 80 NE - CZ - NH2 ANGL. DEV. = -9.5 DEGREES REMARK 500 TRP A 118 CD1 - CG - CD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 TRP A 118 CE2 - CD2 - CG ANGL. DEV. = -5.9 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 48 -76.59 -139.61 REMARK 500 ARG A 87 -169.73 -163.34 REMARK 500 HIS A 92 44.77 -101.90 REMARK 500 THR A 95 -85.13 -120.19 REMARK 500 ASN A 105 76.06 -110.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF SUCCINYL-ALA-PRO-ALA REMARK 800 -P-NITROANILIDE DBREF 1LOP A 1 164 UNP P23869 PPIB_ECOLI 1 164 DBREF 1LOP B 0 4 PDB 1LOP 1LOP 0 4 SEQADV 1LOP GLU A 132 UNP P23869 VAL 132 CONFLICT SEQRES 1 A 164 MET VAL THR PHE HIS THR ASN HIS GLY ASP ILE VAL ILE SEQRES 2 A 164 LYS THR PHE ASP ASP LYS ALA PRO GLU THR VAL LYS ASN SEQRES 3 A 164 PHE LEU ASP TYR CYS ARG GLU GLY PHE TYR ASN ASN THR SEQRES 4 A 164 ILE PHE HIS ARG VAL ILE ASN GLY PHE MET ILE GLN GLY SEQRES 5 A 164 GLY GLY PHE GLU PRO GLY MET LYS GLN LYS ALA THR LYS SEQRES 6 A 164 GLU PRO ILE LYS ASN GLU ALA ASN ASN GLY LEU LYS ASN SEQRES 7 A 164 THR ARG GLY THR LEU ALA MET ALA ARG THR GLN ALA PRO SEQRES 8 A 164 HIS SER ALA THR ALA GLN PHE PHE ILE ASN VAL VAL ASP SEQRES 9 A 164 ASN ASP PHE LEU ASN PHE SER GLY GLU SER LEU GLN GLY SEQRES 10 A 164 TRP GLY TYR CYS VAL PHE ALA GLU VAL VAL ASP GLY MET SEQRES 11 A 164 ASP GLU VAL ASP LYS ILE LYS GLY VAL ALA THR GLY ARG SEQRES 12 A 164 SER GLY MET HIS GLN ASP VAL PRO LYS GLU ASP VAL ILE SEQRES 13 A 164 ILE GLU SER VAL THR VAL SER GLU SEQRES 1 B 5 SIN ALA PRO ALA NIT HET SIN B 0 7 HET NIT B 4 11 HETNAM SIN SUCCINIC ACID HETNAM NIT 4-NITROANILINE HETSYN NIT PARANITROANILINE FORMUL 2 SIN C4 H6 O4 FORMUL 2 NIT C6 H6 N2 O2 FORMUL 3 HOH *133(H2 O) HELIX 1 H1 PHE A 16 ALA A 20 5 5 HELIX 2 H2 PRO A 21 GLU A 33 1 13 HELIX 3 H3 ASN A 105 LEU A 108 5 4 HELIX 4 H4 GLY A 129 LYS A 137 1 9 SHEET 1 A 9 MET A 1 HIS A 5 0 SHEET 2 A 9 ASP A 10 THR A 15 -1 N ILE A 13 O VAL A 2 SHEET 3 A 9 CYS A 121 ASP A 128 -1 N ASP A 128 O VAL A 12 SHEET 4 A 9 GLY A 81 ALA A 86 -1 N LEU A 83 O PHE A 123 SHEET 5 A 9 GLN A 97 VAL A 102 -1 N PHE A 99 O ALA A 84 SHEET 6 A 9 MET A 49 GLY A 52 -1 N GLY A 52 O PHE A 98 SHEET 7 A 9 ASN A 38 VAL A 44 -1 SHEET 8 A 9 VAL A 155 SER A 163 -1 SHEET 9 A 9 MET A 1 HIS A 5 -1 N HIS A 5 O GLU A 158 SHEET 1 B 2 GLY A 142 ARG A 143 0 SHEET 2 B 2 GLN A 148 ASP A 149 -1 LINK C4 SIN B 0 N ALA B 1 1555 1555 1.32 LINK N1 NIT B 4 C ALA B 3 1555 1555 1.34 CISPEP 1 ALA B 1 PRO B 2 0 1.25 SITE 1 AC1 19 ARG A 43 ILE A 45 PHE A 48 MET A 49 SITE 2 AC1 19 ALA A 86 ARG A 87 THR A 88 ALA A 90 SITE 3 AC1 19 HIS A 92 SER A 93 PHE A 99 ASP A 106 SITE 4 AC1 19 PHE A 107 TYR A 120 HOH A 277 HOH B 299 SITE 5 AC1 19 HOH B 349 HOH B 354 HOH B 355 CRYST1 66.330 68.230 40.030 90.00 90.00 90.00 P 21 21 21 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 0.015076 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024981 0.00000