PDB Short entry for 5CBW HEADER ISOMERASE 01-JUL-15 5CBW TITLE HUMAN CYCLOPHILIN D COMPLEXED WITH INHIBITOR. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPIASE F,CYCLOPHILIN D,CYPD,CYCLOPHILIN F,MITOCHONDRIAL COMPND 5 CYCLOPHILIN,CYP-M,ROTAMASE F; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PPIF, CYP3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS CYCOPHILIN, INHIBITOR, ISOMERASE, COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.P.GIBSON,E.SHORE,N.KERSHAW,M.AWAIS,A.JAVED,D.LATAWIEC, AUTHOR 2 S.PANDALANENI,L.WEN,N.BERRY,P.O'NEILL,R.SUTTON,L.Y.LIAN REVDAT 2 10-JAN-24 5CBW 1 LINK REVDAT 1 20-JUL-16 5CBW 0 JRNL AUTH R.P.GIBSON,E.SHORE,N.KERSHAW,M.AWAIS,A.JAVED,D.LATAWIEC, JRNL AUTH 2 S.PANDALANENI,L.WEN,N.BERRY,P.O'NEILL,R.SUTTON,L.Y.LIAN JRNL TITL HUMAN CYCLOPHILIN D COMPLEXED WITH INHIBITOR. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0123 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 16967 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 916 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1123 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.1730 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1240 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 161 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.01000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.116 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.250 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1311 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1260 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1754 ; 2.093 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2910 ; 1.127 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 163 ; 6.878 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 52 ;34.263 ;24.231 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 213 ;12.525 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;19.006 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 186 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1476 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 301 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 655 ; 1.597 ; 1.708 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 656 ; 1.597 ; 1.712 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 817 ; 2.135 ; 2.553 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 818 ; 2.135 ; 2.554 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 656 ; 2.515 ; 2.004 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 657 ; 2.513 ; 2.009 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 938 ; 3.564 ; 2.866 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1525 ; 5.532 ;15.305 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1526 ; 5.536 ;15.325 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5CBW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000210723. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.984 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15607 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 38.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.7 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : 0.02100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.05300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 13.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2BIT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4M POTASSIUM FORMATE, 0.1M BIS-TRIS REMARK 280 PROPANE PH 9, 2% W/V PEG2000MME, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 57.25100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.63250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.63250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 85.87650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.63250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.63250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.62550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.63250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.63250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 85.87650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.63250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.63250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.62550 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.25100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 6.0 KCAL/MOL 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 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 K K A 201 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 420 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 MET A 1 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 O HOH A 393 O HOH A 441 1.73 REMARK 500 O5 PG4 A 204 O HOH A 301 2.05 REMARK 500 OD1 ASP A 11 O HOH A 302 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 439 O HOH A 439 7555 1.72 REMARK 500 O HOH A 340 O HOH A 397 3444 1.77 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 37 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 55 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 151 NE - CZ - NH1 ANGL. DEV. = -3.2 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 ASN A 13 48.01 39.75 REMARK 500 PHE A 60 -77.96 -144.97 REMARK 500 ASN A 71 11.04 -151.19 REMARK 500 THR A 119 51.18 -117.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 202 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 7 OH REMARK 620 2 ASP A 160 OD1 83.9 REMARK 620 3 CYS A 161 O 73.1 76.3 REMARK 620 4 FMT A 203 O1 147.0 88.3 73.9 REMARK 620 5 HOH A 360 O 48.3 131.2 94.9 136.0 REMARK 620 6 HOH A 433 O 103.6 147.2 75.6 67.9 68.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 201 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PGE A 205 O4 REMARK 620 2 PGE A 205 O1 117.1 REMARK 620 3 PGE A 205 O2 111.8 53.8 REMARK 620 4 PGE A 205 O3 54.9 93.2 58.5 REMARK 620 5 PGE A 205 O1 81.7 42.7 87.7 92.0 REMARK 620 6 PGE A 205 O2 75.0 87.7 140.4 123.8 53.8 REMARK 620 7 PGE A 205 O3 123.9 92.0 123.8 174.4 93.2 58.5 REMARK 620 8 PGE A 205 O4 160.8 81.7 75.0 123.9 117.1 111.8 54.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4ZO A 206 DBREF 5CBW A 2 165 UNP P30405 PPIF_HUMAN 44 207 SEQADV 5CBW MET A 1 UNP P30405 INITIATING METHIONINE SEQADV 5CBW ILE A 133 UNP P30405 LYS 175 ENGINEERED MUTATION SEQRES 1 A 165 MET GLY ASN PRO LEU VAL TYR LEU ASP VAL ASP ALA ASN SEQRES 2 A 165 GLY LYS PRO LEU GLY ARG VAL VAL LEU GLU LEU LYS ALA SEQRES 3 A 165 ASP VAL VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU SEQRES 4 A 165 CYS THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER THR SEQRES 5 A 165 PHE HIS ARG VAL ILE PRO SER PHE MET CYS GLN ALA GLY SEQRES 6 A 165 ASP PHE THR ASN HIS ASN GLY THR GLY GLY LYS SER ILE SEQRES 7 A 165 TYR GLY SER ARG PHE PRO ASP GLU ASN PHE THR LEU LYS SEQRES 8 A 165 HIS VAL GLY PRO GLY VAL LEU SER MET ALA ASN ALA GLY SEQRES 9 A 165 PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ILE SEQRES 10 A 165 LYS THR ASP TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY SEQRES 11 A 165 HIS VAL ILE GLU GLY MET ASP VAL VAL LYS LYS ILE GLU SEQRES 12 A 165 SER PHE GLY SER LYS SER GLY ARG THR SER LYS LYS ILE SEQRES 13 A 165 VAL ILE THR ASP CYS GLY GLN LEU SER HET K A 201 1 HET K A 202 1 HET FMT A 203 3 HET PG4 A 204 13 HET PGE A 205 10 HET 4ZO A 206 21 HETNAM K POTASSIUM ION HETNAM FMT FORMIC ACID HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM PGE TRIETHYLENE GLYCOL HETNAM 4ZO ETHYL N-{[4-(ACETYLAMINO)BENZYL]CARBAMOYL}GLYCINATE FORMUL 2 K 2(K 1+) FORMUL 4 FMT C H2 O2 FORMUL 5 PG4 C8 H18 O5 FORMUL 6 PGE C6 H14 O4 FORMUL 7 4ZO C14 H19 N3 O4 FORMUL 8 HOH *161(H2 O) HELIX 1 AA1 VAL A 29 GLY A 42 1 14 HELIX 2 AA2 THR A 119 ASP A 123 5 5 HELIX 3 AA3 GLY A 135 PHE A 145 1 11 SHEET 1 AA1 8 PHE A 53 ILE A 57 0 SHEET 2 AA1 8 MET A 61 ALA A 64 -1 O GLN A 63 N ARG A 55 SHEET 3 AA1 8 PHE A 112 CYS A 115 -1 O PHE A 112 N ALA A 64 SHEET 4 AA1 8 VAL A 97 MET A 100 -1 N SER A 99 O PHE A 113 SHEET 5 AA1 8 VAL A 128 GLU A 134 -1 O GLY A 130 N LEU A 98 SHEET 6 AA1 8 LYS A 15 LEU A 24 -1 N VAL A 21 O ILE A 133 SHEET 7 AA1 8 LEU A 5 ALA A 12 -1 N VAL A 10 O LEU A 17 SHEET 8 AA1 8 ILE A 156 GLN A 163 -1 O ASP A 160 N ASP A 9 LINK OH TYR A 7 K K A 202 1555 1555 3.27 LINK OD1 ASP A 160 K K A 202 1555 1555 2.91 LINK O CYS A 161 K K A 202 1555 1555 2.72 LINK K K A 201 O4 PGE A 205 1555 1555 2.86 LINK K K A 201 O1 PGE A 205 1555 1555 3.43 LINK K K A 201 O2 PGE A 205 1555 1555 2.70 LINK K K A 201 O3 PGE A 205 1555 1555 2.86 LINK K K A 201 O1 PGE A 205 1555 7555 3.43 LINK K K A 201 O2 PGE A 205 1555 7555 2.70 LINK K K A 201 O3 PGE A 205 1555 7555 2.86 LINK K K A 201 O4 PGE A 205 1555 7555 2.86 LINK K K A 202 O1 FMT A 203 1555 1555 2.92 LINK K K A 202 O HOH A 360 1555 1555 3.45 LINK K K A 202 O HOH A 433 1555 1555 2.80 SITE 1 AC1 1 PGE A 205 SITE 1 AC2 5 TYR A 7 ASP A 160 CYS A 161 FMT A 203 SITE 2 AC2 5 HOH A 433 SITE 1 AC3 7 CYS A 40 THR A 41 LYS A 49 CYS A 161 SITE 2 AC3 7 K A 202 HOH A 304 HOH A 330 SITE 1 AC4 6 TYR A 79 VAL A 93 PRO A 95 HIS A 131 SITE 2 AC4 6 HOH A 301 HOH A 405 SITE 1 AC5 5 PRO A 58 SER A 59 TRP A 121 LYS A 148 SITE 2 AC5 5 K A 201 SITE 1 AC6 13 ARG A 55 GLN A 63 GLY A 72 THR A 73 SITE 2 AC6 13 SER A 81 ARG A 82 ALA A 101 ASN A 102 SITE 3 AC6 13 THR A 107 GLN A 111 PHE A 113 HIS A 126 SITE 4 AC6 13 HOH A 398 CRYST1 57.265 57.265 114.502 90.00 90.00 90.00 P 43 21 2 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 0.017463 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017463 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008734 0.00000