HEADER ISOMERASE 14-NOV-96 2NUL TITLE PEPTIDYLPROLYL ISOMERASE FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYLPROLYL ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPTIDYLPROLYL CIS-TRANS ISOMERASE, CYCLOPHILIN; COMPND 5 EC: 5.2.1.8 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS ISOMERASE, ROTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR K.J.EDWARDS,D.L.OLLIS REVDAT 4 09-AUG-23 2NUL 1 ATOM REVDAT 3 16-NOV-11 2NUL 1 VERSN HETATM REVDAT 2 24-FEB-09 2NUL 1 VERSN REVDAT 1 19-NOV-97 2NUL 0 JRNL AUTH K.J.EDWARDS,D.L.OLLIS,N.E.DIXON JRNL TITL CRYSTAL STRUCTURE OF CYTOPLASMIC ESCHERICHIA COLI JRNL TITL 2 PEPTIDYL-PROLYL ISOMERASE: EVIDENCE FOR DECREASED MOBILITY JRNL TITL 3 OF LOOPS UPON COMPLEXATION. JRNL REF J.MOL.BIOL. V. 271 258 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9268657 JRNL DOI 10.1006/JMBI.1997.1151 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 8404 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) : 0.160 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.17 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 754 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 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 : 1217 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.02540 REMARK 3 B22 (A**2) : -7.55150 REMARK 3 B33 (A**2) : -7.55150 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL 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) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 2.003 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.17 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.778 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) : 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NUL 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_1000178417. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUN-96 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : RIGAKU REMARK 200 DATA SCALING SOFTWARE : RIGAKU REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9966 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 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 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 3.1 REMARK 200 STARTING MODEL: PDB ENTRY 1LOP (COORDS RECEIVED FROM AUTHORS IN REMARK 200 ADVANCE OF DEPOSITION) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZED FROM 100 MM TRIS PH 8.5, REMARK 280 0.2 M SODIUM ACETATE, 30% PEG 3.4K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 22.35000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.10000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.35000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.10000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.35000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 34.10000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.35000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 34.10000 REMARK 290 SMTRY3 8 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 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 BIOMT1 2 -1.000000 0.000000 0.000000 44.70000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -51.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 243 LIES ON A SPECIAL POSITION. 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 GLU A 164 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 LYS A 19 CE NZ REMARK 470 LYS A 25 CD CE NZ REMARK 470 ARG A 32 NH1 NH2 REMARK 470 GLU A 33 CG CD OE1 OE2 REMARK 470 ARG A 43 NH1 NH2 REMARK 470 LYS A 60 NZ REMARK 470 GLU A 66 CG CD OE1 OE2 REMARK 470 LYS A 69 CE NZ REMARK 470 LYS A 77 CE NZ REMARK 470 ARG A 80 NH1 NH2 REMARK 470 ARG A 87 NH1 NH2 REMARK 470 GLN A 89 CG CD OE1 NE2 REMARK 470 ASP A 106 CG OD1 OD2 REMARK 470 GLN A 116 CG CD OE1 NE2 REMARK 470 LYS A 135 CE NZ REMARK 470 ARG A 143 NH1 NH2 REMARK 470 GLN A 148 CG CD OE1 NE2 REMARK 470 GLU A 153 CG CD OE1 OE2 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 VAL A 132 CG1 CG2 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 HD22 ASN A 26 H2 HOH A 194 1.28 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 16 69.59 -100.23 REMARK 500 PHE A 48 -70.30 -137.27 REMARK 500 HIS A 92 41.18 -99.22 REMARK 500 THR A 95 -91.03 -126.45 REMARK 500 ASN A 105 74.43 -113.15 REMARK 500 TRP A 118 -37.94 -34.90 REMARK 500 REMARK 500 REMARK: NULL DBREF 2NUL A 1 164 UNP P23869 PPIB_ECOLI 1 164 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 VAL 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 FORMUL 2 HOH *89(H2 O) HELIX 1 1 PRO A 21 ARG A 32 1 12 HELIX 2 2 ALA A 72 ASN A 74 5 3 HELIX 3 3 ASP A 106 LEU A 108 5 3 HELIX 4 4 MET A 130 GLY A 138 1 9 SHEET 1 A 8 ILE A 157 VAL A 162 0 SHEET 2 A 8 VAL A 2 THR A 6 -1 N HIS A 5 O GLU A 158 SHEET 3 A 8 GLY A 9 THR A 15 -1 N ILE A 13 O VAL A 2 SHEET 4 A 8 VAL A 122 ASP A 128 -1 N ASP A 128 O VAL A 12 SHEET 5 A 8 THR A 82 MET A 85 -1 N LEU A 83 O PHE A 123 SHEET 6 A 8 PHE A 98 ASN A 101 -1 N PHE A 99 O ALA A 84 SHEET 7 A 8 MET A 49 GLY A 52 -1 N GLY A 52 O PHE A 98 SHEET 8 A 8 PHE A 41 ILE A 45 -1 N ILE A 45 O MET A 49 CRYST1 44.700 68.200 102.000 90.00 90.00 90.00 C 2 2 21 8 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 0.022371 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014663 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009804 0.00000