HEADER ISOMERASE 01-JUL-15 5CBT 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 FRAGMENT: UNP RESIDUES 44-207; COMPND 5 SYNONYM: PPIASE F,CYCLOPHILIN D,CYPD,CYCLOPHILIN F,MITOCHONDRIAL COMPND 6 CYCLOPHILIN,CYP-M,ROTAMASE F; COMPND 7 EC: 5.2.1.8; COMPND 8 ENGINEERED: 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_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS CYCLOPHILIN, ISOMERASE, COMPLEX, INHIBITOR 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 5CBT 1 LINK REVDAT 1 20-JUL-16 5CBT 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. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 33491 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1767 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2441 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.2700 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 : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14000 REMARK 3 B22 (A**2) : 0.14000 REMARK 3 B33 (A**2) : -0.28000 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): 0.059 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.060 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.035 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.892 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1310 ; 0.031 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1262 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1750 ; 2.774 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2915 ; 1.259 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 163 ; 6.587 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 52 ;33.801 ;24.231 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 213 ;13.423 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;17.040 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 186 ; 0.164 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1468 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 299 ; 0.002 ; 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 ; 1.573 ; 1.412 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 656 ; 1.582 ; 1.414 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 817 ; 2.220 ; 2.120 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 818 ; 2.219 ; 2.121 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 655 ; 3.194 ; 1.726 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 655 ; 3.191 ; 1.726 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 934 ; 4.077 ; 2.440 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1455 ; 5.239 ;12.716 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1456 ; 5.238 ;12.728 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 5CBT 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_1000210113. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-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) : 0.9801 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35342 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.906 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 0.55600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.000 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 (%): 54.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 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 291K 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 57.22750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.92450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.92450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 85.84125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.92450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.92450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.61375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.92450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.92450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 85.84125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.92450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.92450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.61375 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 57.22750 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 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 202 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 389 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 OD1 ASP A 11 O HOH A 301 2.01 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 366 O HOH A 366 7555 1.71 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 GLU A 43 CD GLU A 43 OE1 0.074 REMARK 500 ARG A 55 CD ARG A 55 NE -0.115 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. = -5.5 DEGREES REMARK 500 LYS A 15 CD - CE - NZ ANGL. DEV. = 18.1 DEGREES REMARK 500 ASP A 27 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 37 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 55 NE - CZ - NH1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 55 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 151 NE - CZ - NH2 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 PHE A 60 -80.03 -142.56 REMARK 500 THR A 119 54.09 -116.73 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 203 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 7 OH REMARK 620 2 ASP A 160 OD1 86.0 REMARK 620 3 CYS A 161 O 74.5 76.3 REMARK 620 4 FMT A 204 O1 140.3 92.5 66.6 REMARK 620 5 HOH A 316 O 106.2 145.1 75.8 57.1 REMARK 620 N 1 2 3 4 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 PGE A 207 O4 REMARK 620 2 PGE A 207 O1 144.0 REMARK 620 3 PGE A 207 O2 114.6 63.6 REMARK 620 4 PGE A 207 O3 55.5 105.6 60.1 REMARK 620 5 PGE A 207 O1 96.2 52.7 101.5 97.0 REMARK 620 6 PGE A 207 O2 73.9 101.5 164.3 123.9 63.6 REMARK 620 7 PGE A 207 O3 110.1 97.0 123.9 154.7 105.6 60.1 REMARK 620 8 PGE A 207 O4 118.5 96.2 73.9 110.1 144.0 114.6 55.5 REMARK 620 9 HOH A 389 O 59.2 153.6 97.8 77.4 153.6 97.8 77.4 59.2 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4ZL 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 K A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 207 DBREF 5CBT A 2 165 UNP P30405 PPIF_HUMAN 44 207 SEQADV 5CBT MET A 1 UNP P30405 INITIATING METHIONINE SEQADV 5CBT ILE A 133 UNP P30405 LYS 175 CONFLICT 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 4ZL A 201 17 HET K A 202 1 HET K A 203 1 HET FMT A 204 3 HET PG4 A 205 13 HET EDO A 206 4 HET PGE A 207 10 HETNAM 4ZL ETHYL N-(BENZYLCARBAMOYL)GLYCINATE HETNAM K POTASSIUM ION HETNAM FMT FORMIC ACID HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM EDO 1,2-ETHANEDIOL HETNAM PGE TRIETHYLENE GLYCOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 4ZL C12 H16 N2 O3 FORMUL 3 K 2(K 1+) FORMUL 5 FMT C H2 O2 FORMUL 6 PG4 C8 H18 O5 FORMUL 7 EDO C2 H6 O2 FORMUL 8 PGE C6 H14 O4 FORMUL 9 HOH *123(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 ILE A 114 N CYS A 62 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 PHE A 129 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 203 1555 1555 3.28 LINK OD1 ASP A 160 K K A 203 1555 1555 2.92 LINK O CYS A 161 K K A 203 1555 1555 2.69 LINK K K A 202 O4 PGE A 207 1555 1555 2.97 LINK K K A 202 O1 PGE A 207 1555 1555 2.96 LINK K K A 202 O2 PGE A 207 1555 1555 2.63 LINK K K A 202 O3 PGE A 207 1555 1555 2.83 LINK K K A 202 O1 PGE A 207 1555 7555 2.96 LINK K K A 202 O2 PGE A 207 1555 7555 2.63 LINK K K A 202 O3 PGE A 207 1555 7555 2.83 LINK K K A 202 O4 PGE A 207 1555 7555 2.97 LINK K K A 202 O HOH A 389 1555 1555 2.97 LINK K K A 202 O HOH A 389 1555 7555 2.97 LINK K K A 203 O1 FMT A 204 1555 1555 2.85 LINK K K A 203 O HOH A 316 1555 1555 2.74 SITE 1 AC1 10 ARG A 55 GLN A 63 GLY A 72 ALA A 101 SITE 2 AC1 10 ASN A 102 GLN A 111 PHE A 113 HIS A 126 SITE 3 AC1 10 HOH A 358 HOH A 366 SITE 1 AC2 2 PGE A 207 HOH A 389 SITE 1 AC3 5 TYR A 7 ASP A 160 CYS A 161 FMT A 204 SITE 2 AC3 5 HOH A 316 SITE 1 AC4 8 CYS A 40 THR A 41 LYS A 49 CYS A 161 SITE 2 AC4 8 K A 203 HOH A 312 HOH A 315 HOH A 316 SITE 1 AC5 4 TYR A 79 PRO A 95 HIS A 131 HOH A 353 SITE 1 AC6 6 ASP A 85 GLU A 86 HOH A 306 HOH A 326 SITE 2 AC6 6 HOH A 386 HOH A 395 SITE 1 AC7 6 PRO A 58 SER A 59 TRP A 121 LYS A 148 SITE 2 AC7 6 K A 202 HOH A 389 CRYST1 57.849 57.849 114.455 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 0.017286 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017286 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008737 0.00000