HEADER ELECTRON TRANSPORT 20-NOV-12 3ZCF TITLE STRUCTURE OF RECOMBINANT HUMAN CYTOCHROME C COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C; COMPND 3 CHAIN: A, B, C, D; COMPND 4 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ELECTRON TRANSPORT, RESPIRATION, APOPTOSIS, ELECTRON TRANSFER EXPDTA X-RAY DIFFRACTION AUTHOR B.S.RAJAGOPAL,J.A.R.WORRALL,M.A.HOUGH REVDAT 4 23-OCT-24 3ZCF 1 REMARK REVDAT 3 20-DEC-23 3ZCF 1 REMARK LINK REVDAT 2 11-DEC-13 3ZCF 1 JRNL REVDAT 1 23-OCT-13 3ZCF 0 JRNL AUTH B.S.RAJAGOPAL,A.N.EDZUMA,M.A.HOUGH,K.L.I.M.BLUNDELL, JRNL AUTH 2 V.E.KAGAN,A.A.KAPRALOV,L.A.FRASER,J.N.BUTT,G.G.SILKSTONE, JRNL AUTH 3 M.T.WILSON,D.A.SVISTUNENKO,J.A.R.WORRALL JRNL TITL THE HYDROGEN PEROXIDE INDUCED RADICAL BEHAVIOUR IN HUMAN JRNL TITL 2 CYTOCHROME C PHOSPHOLIPID COMPLEXES: IMPLICATIONS FOR THE JRNL TITL 3 ENHANCED PRO-APOPTOTIC ACTIVITY OF THE G41S MUTANT JRNL REF BIOCHEM.J. V. 456 441 2013 JRNL REFN ISSN 0264-6021 JRNL PMID 24099549 JRNL DOI 10.1042/BJ20130758 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 44527 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2378 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2875 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 165 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3264 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 172 REMARK 3 SOLVENT ATOMS : 344 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.18000 REMARK 3 B22 (A**2) : -1.89000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : -0.20000 REMARK 3 B13 (A**2) : 0.47000 REMARK 3 B23 (A**2) : -0.05000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.074 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.205 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 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): 3528 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3370 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4806 ; 1.640 ; 2.038 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7771 ; 0.860 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 435 ; 6.704 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 131 ;32.657 ;24.809 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 630 ;12.270 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;26.396 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 479 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4019 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 803 ; 0.010 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 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 3ZCF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1290054837. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97620 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46913 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 57.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 100.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: PDB ENTRY 3NWV REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26 TO 31 % W/V POLYETHYLENE GLYCOL REMARK 280 1000 AND 40 MM KH2PO4, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLU A 4 OE2 REMARK 480 MET A 12 CE REMARK 480 LYS A 25 CE NZ REMARK 480 LYS A 39 CE NZ REMARK 480 LYS A 72 NZ REMARK 480 LYS A 86 CD CE NZ REMARK 480 LYS A 87 CD CE NZ REMARK 480 LYS A 88 NZ REMARK 480 LYS B 8 CD CE NZ REMARK 480 LYS B 22 CE NZ REMARK 480 LYS B 39 NZ REMARK 480 LYS B 86 CG CD CE NZ REMARK 480 LYS B 87 CD CE NZ REMARK 480 LYS B 88 CD CE NZ REMARK 480 LYS B 99 CE NZ REMARK 480 GLU C 4 CG CD OE1 OE2 REMARK 480 LYS C 7 NZ REMARK 480 LYS C 8 CE NZ REMARK 480 GLU C 21 CG CD OE1 OE2 REMARK 480 LYS C 25 CD CE NZ REMARK 480 LYS C 39 CE NZ REMARK 480 LYS C 73 CE NZ REMARK 480 LYS C 86 CD CE NZ REMARK 480 GLU C 89 CG CD OE1 OE2 REMARK 480 LYS C 100 CE NZ REMARK 480 LYS D 5 NZ REMARK 480 LYS D 7 NZ REMARK 480 LYS D 8 CE NZ REMARK 480 LYS D 22 NZ REMARK 480 LYS D 39 NZ REMARK 480 LYS D 72 NZ REMARK 480 LYS D 87 NZ REMARK 480 LYS D 88 CE NZ REMARK 480 LYS D 100 CG CD CE NZ REMARK 480 GLU D 104 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 OD2 ASP B 93 O HOH B 2073 2.12 REMARK 500 SG CYS D 17 CAC HEC D 105 2.16 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 LYS A 39 CD LYS A 39 CE -0.202 REMARK 500 LYS A 72 CE LYS A 72 NZ -0.237 REMARK 500 LYS A 87 CG LYS A 87 CD -0.282 REMARK 500 LYS A 88 CE LYS A 88 NZ -0.317 REMARK 500 LYS B 22 CD LYS B 22 CE -0.504 REMARK 500 LYS B 39 CE LYS B 39 NZ -1.001 REMARK 500 LYS B 86 CB LYS B 86 CG -0.178 REMARK 500 LYS B 87 CG LYS B 87 CD -0.454 REMARK 500 LYS B 99 CD LYS B 99 CE -0.193 REMARK 500 LYS C 7 CE LYS C 7 NZ -0.191 REMARK 500 GLU C 21 CB GLU C 21 CG -0.141 REMARK 500 LYS C 39 CE LYS C 39 NZ -0.350 REMARK 500 GLU C 89 CB GLU C 89 CG -0.125 REMARK 500 LYS D 7 CE LYS D 7 NZ 0.281 REMARK 500 LYS D 72 CE LYS D 72 NZ -0.180 REMARK 500 LYS D 87 CE LYS D 87 NZ -0.382 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 LYS A 88 CD - CE - NZ ANGL. DEV. = 22.1 DEGREES REMARK 500 LYS B 8 CB - CG - CD ANGL. DEV. = 16.2 DEGREES REMARK 500 LYS B 22 CG - CD - CE ANGL. DEV. = 36.8 DEGREES REMARK 500 LYS B 22 CD - CE - NZ ANGL. DEV. = 17.9 DEGREES REMARK 500 LYS B 39 CD - CE - NZ ANGL. DEV. = 62.1 DEGREES REMARK 500 LYS B 87 CB - CG - CD ANGL. DEV. = 36.0 DEGREES REMARK 500 LYS B 87 CG - CD - CE ANGL. DEV. = 20.5 DEGREES REMARK 500 LYS B 88 CD - CE - NZ ANGL. DEV. = 14.1 DEGREES REMARK 500 LYS C 39 CD - CE - NZ ANGL. DEV. = 14.5 DEGREES REMARK 500 LYS C 86 CG - CD - CE ANGL. DEV. = 18.8 DEGREES REMARK 500 LYS C 100 CD - CE - NZ ANGL. DEV. = -20.1 DEGREES REMARK 500 LYS D 7 CD - CE - NZ ANGL. DEV. = -14.0 DEGREES REMARK 500 ARG D 38 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 LYS D 72 CD - CE - NZ ANGL. DEV. = 22.7 DEGREES REMARK 500 LYS D 87 CD - CE - NZ ANGL. DEV. = 16.5 DEGREES REMARK 500 GLU D 104 CB - CA - C ANGL. DEV. = -25.9 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 LYS A 27 -139.12 -124.33 REMARK 500 ASN A 70 88.16 -163.47 REMARK 500 LYS B 27 -139.77 -122.21 REMARK 500 ASN B 70 87.08 -161.56 REMARK 500 LYS C 27 -140.50 -124.90 REMARK 500 ASN C 70 86.30 -166.68 REMARK 500 LYS D 27 -139.43 -129.33 REMARK 500 ASN D 70 87.39 -162.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 PROTOPORPHYRIN IX CONTAINING FE (HEM): C-TYPE HAEM 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 HEC A 105 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 18 NE2 REMARK 620 2 HEC A 105 NA 89.0 REMARK 620 3 HEC A 105 NB 86.5 90.8 REMARK 620 4 HEC A 105 NC 90.1 178.6 88.1 REMARK 620 5 HEC A 105 ND 92.2 89.4 178.8 91.7 REMARK 620 6 MET A 80 SD 176.3 87.4 94.5 93.5 86.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC B 105 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 18 NE2 REMARK 620 2 HEC B 105 NA 89.3 REMARK 620 3 HEC B 105 NB 87.3 90.4 REMARK 620 4 HEC B 105 NC 89.9 178.8 88.7 REMARK 620 5 HEC B 105 ND 92.6 90.0 179.5 90.9 REMARK 620 6 MET B 80 SD 176.3 87.3 94.1 93.6 86.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC C 105 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 18 NE2 REMARK 620 2 HEC C 105 NA 90.5 REMARK 620 3 HEC C 105 NB 85.3 90.0 REMARK 620 4 HEC C 105 NC 88.9 178.8 88.9 REMARK 620 5 HEC C 105 ND 93.7 90.2 179.0 90.9 REMARK 620 6 MET C 80 SD 177.4 87.6 93.0 93.0 88.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC D 105 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 18 NE2 REMARK 620 2 HEC D 105 NA 89.9 REMARK 620 3 HEC D 105 NB 87.1 90.8 REMARK 620 4 HEC D 105 NC 88.9 178.4 88.1 REMARK 620 5 HEC D 105 ND 92.6 89.4 179.6 91.7 REMARK 620 6 MET D 80 SD 176.7 87.0 94.0 94.3 86.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC B 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC C 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC D 105 DBREF 3ZCF A 1 104 UNP P99999 CYC_HUMAN 2 105 DBREF 3ZCF B 1 104 UNP P99999 CYC_HUMAN 2 105 DBREF 3ZCF C 1 104 UNP P99999 CYC_HUMAN 2 105 DBREF 3ZCF D 1 104 UNP P99999 CYC_HUMAN 2 105 SEQRES 1 A 104 GLY ASP VAL GLU LYS GLY LYS LYS ILE PHE ILE MET LYS SEQRES 2 A 104 CYS SER GLN CYS HIS THR VAL GLU LYS GLY GLY LYS HIS SEQRES 3 A 104 LYS THR GLY PRO ASN LEU HIS GLY LEU PHE GLY ARG LYS SEQRES 4 A 104 THR GLY GLN ALA PRO GLY TYR SER TYR THR ALA ALA ASN SEQRES 5 A 104 LYS ASN LYS GLY ILE ILE TRP GLY GLU ASP THR LEU MET SEQRES 6 A 104 GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY THR SEQRES 7 A 104 LYS MET ILE PHE VAL GLY ILE LYS LYS LYS GLU GLU ARG SEQRES 8 A 104 ALA ASP LEU ILE ALA TYR LEU LYS LYS ALA THR ASN GLU SEQRES 1 B 104 GLY ASP VAL GLU LYS GLY LYS LYS ILE PHE ILE MET LYS SEQRES 2 B 104 CYS SER GLN CYS HIS THR VAL GLU LYS GLY GLY LYS HIS SEQRES 3 B 104 LYS THR GLY PRO ASN LEU HIS GLY LEU PHE GLY ARG LYS SEQRES 4 B 104 THR GLY GLN ALA PRO GLY TYR SER TYR THR ALA ALA ASN SEQRES 5 B 104 LYS ASN LYS GLY ILE ILE TRP GLY GLU ASP THR LEU MET SEQRES 6 B 104 GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY THR SEQRES 7 B 104 LYS MET ILE PHE VAL GLY ILE LYS LYS LYS GLU GLU ARG SEQRES 8 B 104 ALA ASP LEU ILE ALA TYR LEU LYS LYS ALA THR ASN GLU SEQRES 1 C 104 GLY ASP VAL GLU LYS GLY LYS LYS ILE PHE ILE MET LYS SEQRES 2 C 104 CYS SER GLN CYS HIS THR VAL GLU LYS GLY GLY LYS HIS SEQRES 3 C 104 LYS THR GLY PRO ASN LEU HIS GLY LEU PHE GLY ARG LYS SEQRES 4 C 104 THR GLY GLN ALA PRO GLY TYR SER TYR THR ALA ALA ASN SEQRES 5 C 104 LYS ASN LYS GLY ILE ILE TRP GLY GLU ASP THR LEU MET SEQRES 6 C 104 GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY THR SEQRES 7 C 104 LYS MET ILE PHE VAL GLY ILE LYS LYS LYS GLU GLU ARG SEQRES 8 C 104 ALA ASP LEU ILE ALA TYR LEU LYS LYS ALA THR ASN GLU SEQRES 1 D 104 GLY ASP VAL GLU LYS GLY LYS LYS ILE PHE ILE MET LYS SEQRES 2 D 104 CYS SER GLN CYS HIS THR VAL GLU LYS GLY GLY LYS HIS SEQRES 3 D 104 LYS THR GLY PRO ASN LEU HIS GLY LEU PHE GLY ARG LYS SEQRES 4 D 104 THR GLY GLN ALA PRO GLY TYR SER TYR THR ALA ALA ASN SEQRES 5 D 104 LYS ASN LYS GLY ILE ILE TRP GLY GLU ASP THR LEU MET SEQRES 6 D 104 GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY THR SEQRES 7 D 104 LYS MET ILE PHE VAL GLY ILE LYS LYS LYS GLU GLU ARG SEQRES 8 D 104 ALA ASP LEU ILE ALA TYR LEU LYS LYS ALA THR ASN GLU HET HEC A 105 43 HET HEC B 105 43 HET HEC C 105 43 HET HEC D 105 43 HETNAM HEC HEME C FORMUL 5 HEC 4(C34 H34 FE N4 O4) FORMUL 9 HOH *344(H2 O) HELIX 1 1 ASP A 2 CYS A 14 1 13 HELIX 2 2 THR A 49 LYS A 55 1 7 HELIX 3 3 GLY A 60 ASN A 70 1 11 HELIX 4 4 ASN A 70 ILE A 75 1 6 HELIX 5 5 LYS A 87 THR A 102 1 16 HELIX 6 6 ASP B 2 CYS B 14 1 13 HELIX 7 7 THR B 49 LYS B 55 1 7 HELIX 8 8 GLY B 60 ASN B 70 1 11 HELIX 9 9 ASN B 70 ILE B 75 1 6 HELIX 10 10 LYS B 87 THR B 102 1 16 HELIX 11 11 ASP C 2 CYS C 14 1 13 HELIX 12 12 THR C 49 LYS C 55 1 7 HELIX 13 13 GLY C 60 ASN C 70 1 11 HELIX 14 14 ASN C 70 ILE C 75 1 6 HELIX 15 15 LYS C 87 THR C 102 1 16 HELIX 16 16 ASP D 2 CYS D 14 1 13 HELIX 17 17 THR D 49 GLY D 56 1 8 HELIX 18 18 GLY D 60 ASN D 70 1 11 HELIX 19 19 ASN D 70 ILE D 75 1 6 HELIX 20 20 LYS D 87 THR D 102 1 16 LINK SG CYS A 14 CAB HEC A 105 1555 1555 1.97 LINK SG CYS B 14 CAB HEC B 105 1555 1555 2.01 LINK SG CYS C 14 CAB HEC C 105 1555 1555 1.99 LINK SG CYS D 14 CAB HEC D 105 1555 1555 1.92 LINK NE2 HIS A 18 FE HEC A 105 1555 1555 2.05 LINK SD MET A 80 FE HEC A 105 1555 1555 2.26 LINK NE2 HIS B 18 FE HEC B 105 1555 1555 2.08 LINK SD MET B 80 FE HEC B 105 1555 1555 2.30 LINK NE2 HIS C 18 FE HEC C 105 1555 1555 2.14 LINK SD MET C 80 FE HEC C 105 1555 1555 2.25 LINK NE2 HIS D 18 FE HEC D 105 1555 1555 2.03 LINK SD MET D 80 FE HEC D 105 1555 1555 2.30 SITE 1 AC1 24 LYS A 13 CYS A 14 CYS A 17 HIS A 18 SITE 2 AC1 24 THR A 28 GLY A 29 PRO A 30 THR A 40 SITE 3 AC1 24 GLY A 41 TYR A 46 TYR A 48 THR A 49 SITE 4 AC1 24 ASN A 52 TRP A 59 TYR A 67 LEU A 68 SITE 5 AC1 24 THR A 78 LYS A 79 MET A 80 ILE A 81 SITE 6 AC1 24 PHE A 82 ILE A 85 HOH A2055 LYS B 55 SITE 1 AC2 22 LYS B 13 CYS B 14 CYS B 17 HIS B 18 SITE 2 AC2 22 THR B 28 GLY B 29 PRO B 30 THR B 40 SITE 3 AC2 22 GLY B 41 TYR B 46 TYR B 48 THR B 49 SITE 4 AC2 22 ASN B 52 TRP B 59 TYR B 67 LEU B 68 SITE 5 AC2 22 THR B 78 LYS B 79 MET B 80 LEU B 94 SITE 6 AC2 22 HOH B2025 HOH B2029 SITE 1 AC3 22 LYS C 13 CYS C 14 CYS C 17 HIS C 18 SITE 2 AC3 22 THR C 28 PRO C 30 THR C 40 GLY C 41 SITE 3 AC3 22 TYR C 46 TYR C 48 THR C 49 ASN C 52 SITE 4 AC3 22 TRP C 59 TYR C 67 LEU C 68 THR C 78 SITE 5 AC3 22 LYS C 79 MET C 80 LEU C 94 HOH C2020 SITE 6 AC3 22 HOH C2025 LYS D 55 SITE 1 AC4 22 LYS A 55 LYS D 13 CYS D 14 CYS D 17 SITE 2 AC4 22 HIS D 18 THR D 28 PRO D 30 THR D 40 SITE 3 AC4 22 GLY D 41 TYR D 46 TYR D 48 THR D 49 SITE 4 AC4 22 ASN D 52 TRP D 59 TYR D 67 LEU D 68 SITE 5 AC4 22 THR D 78 LYS D 79 MET D 80 ILE D 85 SITE 6 AC4 22 LEU D 94 HOH D2034 CRYST1 36.545 53.915 58.723 76.54 88.57 72.10 P 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 0.027364 -0.008838 0.001449 0.00000 SCALE2 0.000000 0.019491 -0.004747 0.00000 SCALE3 0.000000 0.000000 0.017532 0.00000 CONECT 115 3357 CONECT 146 3335 CONECT 631 3335 CONECT 945 3400 CONECT 982 3378 CONECT 1464 3378 CONECT 1783 3443 CONECT 1820 3421 CONECT 2303 3421 CONECT 2618 3486 CONECT 2649 3464 CONECT 3131 3464 CONECT 3335 146 631 3340 3351 CONECT 3335 3359 3367 CONECT 3336 3341 3371 CONECT 3337 3344 3352 CONECT 3338 3355 3360 CONECT 3339 3363 3368 CONECT 3340 3335 3341 3344 CONECT 3341 3336 3340 3342 CONECT 3342 3341 3343 3346 CONECT 3343 3342 3344 3345 CONECT 3344 3337 3340 3343 CONECT 3345 3343 CONECT 3346 3342 3347 CONECT 3347 3346 3348 CONECT 3348 3347 3349 3350 CONECT 3349 3348 CONECT 3350 3348 CONECT 3351 3335 3352 3355 CONECT 3352 3337 3351 3353 CONECT 3353 3352 3354 3356 CONECT 3354 3353 3355 3357 CONECT 3355 3338 3351 3354 CONECT 3356 3353 CONECT 3357 115 3354 3358 CONECT 3358 3357 CONECT 3359 3335 3360 3363 CONECT 3360 3338 3359 3361 CONECT 3361 3360 3362 3364 CONECT 3362 3361 3363 3365 CONECT 3363 3339 3359 3362 CONECT 3364 3361 CONECT 3365 3362 3366 CONECT 3366 3365 CONECT 3367 3335 3368 3371 CONECT 3368 3339 3367 3369 CONECT 3369 3368 3370 3372 CONECT 3370 3369 3371 3373 CONECT 3371 3336 3367 3370 CONECT 3372 3369 CONECT 3373 3370 3374 CONECT 3374 3373 3375 CONECT 3375 3374 3376 3377 CONECT 3376 3375 CONECT 3377 3375 CONECT 3378 982 1464 3383 3394 CONECT 3378 3402 3410 CONECT 3379 3384 3414 CONECT 3380 3387 3395 CONECT 3381 3398 3403 CONECT 3382 3406 3411 CONECT 3383 3378 3384 3387 CONECT 3384 3379 3383 3385 CONECT 3385 3384 3386 3389 CONECT 3386 3385 3387 3388 CONECT 3387 3380 3383 3386 CONECT 3388 3386 CONECT 3389 3385 3390 CONECT 3390 3389 3391 CONECT 3391 3390 3392 3393 CONECT 3392 3391 CONECT 3393 3391 CONECT 3394 3378 3395 3398 CONECT 3395 3380 3394 3396 CONECT 3396 3395 3397 3399 CONECT 3397 3396 3398 3400 CONECT 3398 3381 3394 3397 CONECT 3399 3396 CONECT 3400 945 3397 3401 CONECT 3401 3400 CONECT 3402 3378 3403 3406 CONECT 3403 3381 3402 3404 CONECT 3404 3403 3405 3407 CONECT 3405 3404 3406 3408 CONECT 3406 3382 3402 3405 CONECT 3407 3404 CONECT 3408 3405 3409 CONECT 3409 3408 CONECT 3410 3378 3411 3414 CONECT 3411 3382 3410 3412 CONECT 3412 3411 3413 3415 CONECT 3413 3412 3414 3416 CONECT 3414 3379 3410 3413 CONECT 3415 3412 CONECT 3416 3413 3417 CONECT 3417 3416 3418 CONECT 3418 3417 3419 3420 CONECT 3419 3418 CONECT 3420 3418 CONECT 3421 1820 2303 3426 3437 CONECT 3421 3445 3453 CONECT 3422 3427 3457 CONECT 3423 3430 3438 CONECT 3424 3441 3446 CONECT 3425 3449 3454 CONECT 3426 3421 3427 3430 CONECT 3427 3422 3426 3428 CONECT 3428 3427 3429 3432 CONECT 3429 3428 3430 3431 CONECT 3430 3423 3426 3429 CONECT 3431 3429 CONECT 3432 3428 3433 CONECT 3433 3432 3434 CONECT 3434 3433 3435 3436 CONECT 3435 3434 CONECT 3436 3434 CONECT 3437 3421 3438 3441 CONECT 3438 3423 3437 3439 CONECT 3439 3438 3440 3442 CONECT 3440 3439 3441 3443 CONECT 3441 3424 3437 3440 CONECT 3442 3439 CONECT 3443 1783 3440 3444 CONECT 3444 3443 CONECT 3445 3421 3446 3449 CONECT 3446 3424 3445 3447 CONECT 3447 3446 3448 3450 CONECT 3448 3447 3449 3451 CONECT 3449 3425 3445 3448 CONECT 3450 3447 CONECT 3451 3448 3452 CONECT 3452 3451 CONECT 3453 3421 3454 3457 CONECT 3454 3425 3453 3455 CONECT 3455 3454 3456 3458 CONECT 3456 3455 3457 3459 CONECT 3457 3422 3453 3456 CONECT 3458 3455 CONECT 3459 3456 3460 CONECT 3460 3459 3461 CONECT 3461 3460 3462 3463 CONECT 3462 3461 CONECT 3463 3461 CONECT 3464 2649 3131 3469 3480 CONECT 3464 3488 3496 CONECT 3465 3470 3500 CONECT 3466 3473 3481 CONECT 3467 3484 3489 CONECT 3468 3492 3497 CONECT 3469 3464 3470 3473 CONECT 3470 3465 3469 3471 CONECT 3471 3470 3472 3475 CONECT 3472 3471 3473 3474 CONECT 3473 3466 3469 3472 CONECT 3474 3472 CONECT 3475 3471 3476 CONECT 3476 3475 3477 CONECT 3477 3476 3478 3479 CONECT 3478 3477 CONECT 3479 3477 CONECT 3480 3464 3481 3484 CONECT 3481 3466 3480 3482 CONECT 3482 3481 3483 3485 CONECT 3483 3482 3484 3486 CONECT 3484 3467 3480 3483 CONECT 3485 3482 CONECT 3486 2618 3483 3487 CONECT 3487 3486 CONECT 3488 3464 3489 3492 CONECT 3489 3467 3488 3490 CONECT 3490 3489 3491 3493 CONECT 3491 3490 3492 3494 CONECT 3492 3468 3488 3491 CONECT 3493 3490 CONECT 3494 3491 3495 CONECT 3495 3494 CONECT 3496 3464 3497 3500 CONECT 3497 3468 3496 3498 CONECT 3498 3497 3499 3501 CONECT 3499 3498 3500 3502 CONECT 3500 3465 3496 3499 CONECT 3501 3498 CONECT 3502 3499 3503 CONECT 3503 3502 3504 CONECT 3504 3503 3505 3506 CONECT 3505 3504 CONECT 3506 3504 MASTER 466 0 4 20 0 0 24 6 3780 4 188 32 END