HEADER OXIDOREDUCTASE 22-FEB-13 3ZOO TITLE STRUCTURE OF THE Y46F MUTANT OF HUMAN CYTOCHROME C COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: 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 OXIDOREDUCTASE, RESPIRATION, APOPTOSIS, ELECTRON TRANSFER EXPDTA X-RAY DIFFRACTION AUTHOR B.S.RAJAGOPAL,J.A.R.WORRALL,M.A.HOUGH REVDAT 4 20-DEC-23 3ZOO 1 REMARK LINK REVDAT 3 11-NOV-15 3ZOO 1 REMARK HET HETNAM HETSYN REVDAT 3 2 1 FORMUL LINK ATOM ANISOU REVDAT 3 3 1 HETATM CONECT MASTER REVDAT 2 11-DEC-13 3ZOO 1 JRNL REVDAT 1 23-OCT-13 3ZOO 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. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 81707 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) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4338 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5170 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 233 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3260 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 182 REMARK 3 SOLVENT ATOMS : 417 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.51000 REMARK 3 B22 (A**2) : -0.13000 REMARK 3 B33 (A**2) : 0.08000 REMARK 3 B12 (A**2) : 1.24000 REMARK 3 B13 (A**2) : -1.43000 REMARK 3 B23 (A**2) : -0.16000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.056 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.055 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.408 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3608 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3454 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4920 ; 1.990 ; 2.036 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7991 ; 1.279 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 453 ; 7.177 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;34.569 ;25.113 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 656 ;12.429 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;18.404 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 486 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4135 ; 0.015 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 823 ; 0.020 ; 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): 7062 ; 4.001 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 92 ;32.699 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7277 ;15.951 ; 5.000 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 3ZOO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1290055442. 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 : SI MONOCHROMATOR 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 : 86068 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 30.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -10.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3NWV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26-31% (W/V) PEG 1000, 40 MM KH2PO4 PH REMARK 280 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 MET A 12 CE REMARK 480 GLN A 16 NE2 REMARK 480 LYS A 25 CE NZ REMARK 480 LYS A 39 CE NZ REMARK 480 LYS A 53 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 CE NZ REMARK 480 GLU A 89 CG CD OE1 OE2 REMARK 480 LYS B 22 CD CE NZ REMARK 480 LYS B 39 NZ REMARK 480 LYS B 86 CE NZ REMARK 480 LYS B 87 CD CE NZ REMARK 480 LYS B 88 CE NZ REMARK 480 GLU C 4 OE1 REMARK 480 LYS C 8 CE NZ REMARK 480 MET C 12 CE REMARK 480 LYS C 25 CD CE NZ REMARK 480 LYS C 39 CD CE NZ REMARK 480 LYS C 86 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 8 CE NZ REMARK 480 LYS D 39 CE NZ REMARK 480 LYS D 72 NZ REMARK 480 LYS D 88 CE NZ REMARK 480 LYS D 100 CE NZ REMARK 480 GLU D 104 CB CG CD OE1 OE2 OXT 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 2141 O HOH B 2012 1465 2.13 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 -0.153 REMARK 500 LYS A 39 CE LYS A 39 NZ -0.448 REMARK 500 LYS A 88 CD LYS A 88 CE -0.162 REMARK 500 LYS B 39 CE LYS B 39 NZ -0.185 REMARK 500 LYS B 87 CG LYS B 87 CD -0.411 REMARK 500 LYS B 88 CD LYS B 88 CE -0.320 REMARK 500 LYS B 88 CE LYS B 88 NZ -0.177 REMARK 500 GLU C 4 CD GLU C 4 OE1 0.097 REMARK 500 GLU C 89 CB GLU C 89 CG -0.187 REMARK 500 LYS D 5 CE LYS D 5 NZ -0.293 REMARK 500 LYS D 39 CD LYS D 39 CE -0.238 REMARK 500 LYS D 88 CD LYS D 88 CE -0.186 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 25 CG - CD - CE ANGL. DEV. = 19.7 DEGREES REMARK 500 LYS A 72 CD - CE - NZ ANGL. DEV. = 21.5 DEGREES REMARK 500 LYS B 87 CB - CG - CD ANGL. DEV. = 52.1 DEGREES REMARK 500 LYS B 87 CG - CD - CE ANGL. DEV. = 43.4 DEGREES REMARK 500 LYS B 88 CD - CE - NZ ANGL. DEV. = 27.2 DEGREES REMARK 500 GLY C 24 N - CA - C ANGL. DEV. = 16.4 DEGREES REMARK 500 LYS D 5 CD - CE - NZ ANGL. DEV. = 26.5 DEGREES REMARK 500 LYS D 39 CG - CD - CE ANGL. DEV. = 19.9 DEGREES REMARK 500 ARG D 91 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 LYS A 27 -137.10 -129.81 REMARK 500 ASN A 70 87.10 -161.79 REMARK 500 LYS B 27 -139.16 -120.83 REMARK 500 LYS B 27 -139.32 -120.86 REMARK 500 ASN B 70 86.29 -162.20 REMARK 500 LYS C 25 117.04 -9.09 REMARK 500 LYS C 25 117.04 63.90 REMARK 500 LYS C 27 -138.38 -115.29 REMARK 500 ASN C 70 90.48 -162.09 REMARK 500 LYS D 27 -139.50 -129.45 REMARK 500 ASN D 70 83.72 -161.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY C 24 LYS C 25 143.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2067 DISTANCE = 6.44 ANGSTROMS 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 89.3 REMARK 620 3 HEC A 105 NB 87.3 90.7 REMARK 620 4 HEC A 105 NC 90.6 179.5 88.8 REMARK 620 5 HEC A 105 ND 92.0 89.8 179.2 90.8 REMARK 620 6 MET A 80 SD 175.8 86.6 93.5 93.5 87.2 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 89.9 REMARK 620 3 HEC B 105 NB 87.8 88.9 REMARK 620 4 HEC B 105 NC 90.1 179.1 90.2 REMARK 620 5 HEC B 105 ND 90.9 91.2 178.6 89.7 REMARK 620 6 MET B 80 SD 175.9 86.5 93.9 93.6 87.4 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 85.1 REMARK 620 3 HEC C 105 NB 89.7 88.9 REMARK 620 4 HEC C 105 NC 94.3 178.6 89.8 REMARK 620 5 HEC C 105 ND 89.4 91.4 179.1 90.0 REMARK 620 6 MET C 80 SD 171.8 87.6 93.9 93.1 87.0 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 88.5 REMARK 620 3 HEC D 105 NB 89.7 90.8 REMARK 620 4 HEC D 105 NC 91.3 178.8 88.0 REMARK 620 5 HEC D 105 ND 88.9 89.3 178.6 91.9 REMARK 620 6 MET D 80 SD 173.9 86.1 93.3 94.2 88.1 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1106 DBREF 3ZOO A 1 104 UNP P99999 CYC_HUMAN 2 105 DBREF 3ZOO B 1 104 UNP P99999 CYC_HUMAN 2 105 DBREF 3ZOO C 1 104 UNP P99999 CYC_HUMAN 2 105 DBREF 3ZOO D 1 104 UNP P99999 CYC_HUMAN 2 105 SEQADV 3ZOO PHE A 46 UNP P99999 TYR 47 ENGINEERED MUTATION SEQADV 3ZOO PHE B 46 UNP P99999 TYR 47 ENGINEERED MUTATION SEQADV 3ZOO PHE C 46 UNP P99999 TYR 47 ENGINEERED MUTATION SEQADV 3ZOO PHE D 46 UNP P99999 TYR 47 ENGINEERED MUTATION 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 PHE 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 PHE 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 PHE 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 PHE 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 PO4 A1105 5 HET PO4 A1106 5 HET HEC B 105 43 HET HEC C 105 43 HET HEC D 105 43 HETNAM HEC HEME C HETNAM PO4 PHOSPHATE ION FORMUL 5 HEC 4(C34 H34 FE N4 O4) FORMUL 6 PO4 2(O4 P 3-) FORMUL 11 HOH *417(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 GLU B 104 1 18 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 LYS D 55 1 7 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 1.93 LINK SG CYS A 17 CAC HEC A 105 1555 1555 2.06 LINK SG CYS B 14 CAB HEC B 105 1555 1555 1.96 LINK SG CYS B 17 CAC HEC B 105 1555 1555 2.21 LINK SG CYS C 14 CAB HEC C 105 1555 1555 1.96 LINK SG CYS C 17 CAC HEC C 105 1555 1555 2.16 LINK SG CYS D 14 CAB HEC D 105 1555 1555 1.94 LINK SG CYS D 17 CAC HEC D 105 1555 1555 2.08 LINK NE2 HIS A 18 FE HEC A 105 1555 1555 2.00 LINK SD MET A 80 FE HEC A 105 1555 1555 2.29 LINK NE2 HIS B 18 FE HEC B 105 1555 1555 2.06 LINK SD MET B 80 FE HEC B 105 1555 1555 2.29 LINK NE2 HIS C 18 FE HEC C 105 1555 1555 2.01 LINK SD MET C 80 FE HEC C 105 1555 1555 2.25 LINK NE2 HIS D 18 FE HEC D 105 1555 1555 2.02 LINK SD MET D 80 FE HEC D 105 1555 1555 2.29 SITE 1 AC1 20 LYS A 13 CYS A 14 CYS A 17 HIS A 18 SITE 2 AC1 20 THR A 28 PRO A 30 THR A 40 GLY A 41 SITE 3 AC1 20 TYR A 48 THR A 49 ASN A 52 TRP A 59 SITE 4 AC1 20 TYR A 67 LEU A 68 THR A 78 LYS A 79 SITE 5 AC1 20 MET A 80 PHE A 82 HOH A2070 LYS B 55 SITE 1 AC2 20 LYS B 13 CYS B 14 CYS B 17 HIS B 18 SITE 2 AC2 20 THR B 28 GLY B 29 PRO B 30 THR B 40 SITE 3 AC2 20 GLY B 41 TYR B 48 THR B 49 ASN B 52 SITE 4 AC2 20 TRP B 59 TYR B 67 THR B 78 LYS B 79 SITE 5 AC2 20 MET B 80 PHE B 82 HOH B2030 HOH B2034 SITE 1 AC3 21 LYS C 13 CYS C 14 CYS C 17 HIS C 18 SITE 2 AC3 21 THR C 28 PRO C 30 THR C 40 GLY C 41 SITE 3 AC3 21 TYR C 48 THR C 49 ASN C 52 TRP C 59 SITE 4 AC3 21 TYR C 67 LEU C 68 THR C 78 LYS C 79 SITE 5 AC3 21 MET C 80 PHE C 82 HOH C2031 HOH C2035 SITE 6 AC3 21 LYS D 55 SITE 1 AC4 21 LYS A 55 LYS D 13 CYS D 14 CYS D 17 SITE 2 AC4 21 HIS D 18 THR D 28 PRO D 30 THR D 40 SITE 3 AC4 21 GLY D 41 TYR D 48 THR D 49 ASN D 52 SITE 4 AC4 21 TRP D 59 TYR D 67 THR D 78 LYS D 79 SITE 5 AC4 21 MET D 80 ILE D 81 PHE D 82 ILE D 85 SITE 6 AC4 21 HOH D2042 SITE 1 AC5 7 LYS A 87 LYS A 88 HOH A2087 HOH A2126 SITE 2 AC5 7 HOH A2144 HOH A2145 LYS D 79 SITE 1 AC6 2 LYS A 13 LYS B 73 CRYST1 36.367 53.952 58.950 76.55 88.73 71.86 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 0.027497 -0.009009 0.001576 0.00000 SCALE2 0.000000 0.019504 -0.004770 0.00000 SCALE3 0.000000 0.000000 0.017468 0.00000