HEADER ELECTRON TRANSPORT 12-JUN-15 5C0Z TITLE THE STRUCTURE OF OXIDIZED RAT CYTOCHROME C AT 1.13 ANGSTROMS TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C, SOMATIC; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 TISSUE: SOMATIC; SOURCE 6 GENE: CYCS; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: C41 (DE3); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PLW01 KEYWDS CYTOCHROME OXIDIZED RAT NATIVE, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR B.F.P.EDWARDS,G.MAHAPATRA,A.A.VAISHNAV,J.S.BRUNZELLE,M.HUTTEMANN REVDAT 5 27-SEP-23 5C0Z 1 REMARK REVDAT 4 25-DEC-19 5C0Z 1 REMARK REVDAT 3 23-OCT-19 5C0Z 1 JRNL LINK REVDAT 2 06-SEP-17 5C0Z 1 REMARK REVDAT 1 21-SEP-16 5C0Z 0 JRNL AUTH H.A.KALPAGE,A.VAISHNAV,J.LIU,A.VARUGHESE,J.WAN,A.A.TURNER, JRNL AUTH 2 Q.JI,M.P.ZUREK,A.A.KAPRALOV,V.E.KAGAN,J.S.BRUNZELLE, JRNL AUTH 3 M.A.RECANATI,L.I.GROSSMAN,T.H.SANDERSON,I.LEE,A.R.SALOMON, JRNL AUTH 4 B.F.P.EDWARDS,M.HUTTEMANN JRNL TITL SERINE-47 PHOSPHORYLATION OF CYTOCHROMECIN THE MAMMALIAN JRNL TITL 2 BRAIN REGULATES CYTOCHROMECOXIDASE AND CASPASE-3 ACTIVITY. JRNL REF FASEB J. 1120R 2019 JRNL REFN ESSN 1530-6860 JRNL PMID 31570002 JRNL DOI 10.1096/FJ.201901120R REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.PECINA,G.G.BORISENKO,N.A.BELIKOVA,Y.Y.TYURINA,A.PECINOVA, REMARK 1 AUTH 2 I.LEE,A.K.SAMHAN-ARIAS,K.PRZYKLENK,V.E.KAGAN,M.HUTTEMANN REMARK 1 TITL PHOSPHOMIMETIC SUBSTITUTION OF CYTOCHROME C TYROSINE 48 REMARK 1 TITL 2 DECREASES RESPIRATION AND BINDING TO CARDIOLIPIN AND REMARK 1 TITL 3 ABOLISHES ABILITY TO TRIGGER DOWNSTREAM CASPASE ACTIVATION. REMARK 1 REF BIOCHEMISTRY V. 49 6705 2010 REMARK 1 REFN ISSN 1520-4995 REMARK 1 PMID 20586425 REMARK 1 DOI 10.1021/BI100486S REMARK 2 REMARK 2 RESOLUTION. 1.12 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) : 1.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.4 REMARK 3 NUMBER OF REFLECTIONS : 127840 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) : 0.133 REMARK 3 R VALUE (WORKING SET) : 0.132 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6713 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) : 1.12 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4841 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 44.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE SET COUNT : 240 REMARK 3 BIN FREE R VALUE : 0.2400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3228 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 224 REMARK 3 SOLVENT ATOMS : 537 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.75000 REMARK 3 B22 (A**2) : -0.24000 REMARK 3 B33 (A**2) : -0.62000 REMARK 3 B12 (A**2) : -0.17000 REMARK 3 B13 (A**2) : 0.45000 REMARK 3 B23 (A**2) : 0.31000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.033 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.034 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.023 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.096 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3605 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3440 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4906 ; 1.903 ; 2.063 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7960 ; 1.182 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 424 ; 6.732 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;32.761 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 668 ;11.439 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;31.488 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 467 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3988 ; 0.018 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 806 ; 0.016 ; 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): 1672 ; 1.080 ; 1.327 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1671 ; 1.079 ; 1.327 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2086 ; 1.378 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2087 ; 1.378 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1933 ; 1.547 ; 1.509 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1859 ; 1.542 ; 1.502 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2688 ; 1.854 ; 2.123 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4897 ; 3.493 ;12.232 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4574 ; 2.770 ;11.245 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7045 ; 2.513 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 122 ;31.971 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7378 ;10.542 ; 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 : 1.30 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5C0Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210579. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 127840 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.124 REMARK 200 RESOLUTION RANGE LOW (A) : 49.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 44.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.54800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.8.1 REMARK 200 STARTING MODEL: 3ZOO REMARK 200 REMARK 200 REMARK: 0.4 MM PRISMS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, ISOPROPANOL, SODIUM ACETATE, REMARK 280 POTASSIUM FERRICYANATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K 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 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 0 REMARK 465 MET B 0 REMARK 465 MET C 0 REMARK 465 MET D 0 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 21 CD GLU A 21 OE1 0.085 REMARK 500 GLU A 21 CD GLU A 21 OE2 0.091 REMARK 500 ARG A 38 CZ ARG A 38 NH2 -0.083 REMARK 500 GLU C 90 CD GLU C 90 OE2 -0.090 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 38 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 38 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 38 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 38 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG D 38 NE - CZ - NH2 ANGL. DEV. = -3.7 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 -137.96 -130.53 REMARK 500 ASN A 70 88.51 -165.02 REMARK 500 LYS B 27 -135.30 -127.95 REMARK 500 ASN B 70 89.71 -167.05 REMARK 500 CYS C 14 -34.85 -130.67 REMARK 500 LYS C 27 -134.69 -124.69 REMARK 500 ASN C 70 86.95 -166.61 REMARK 500 CYS D 14 -35.44 -131.46 REMARK 500 LYS D 27 -134.22 -127.40 REMARK 500 ASN D 70 90.47 -167.88 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 A 451 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A 452 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH A 453 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH C 448 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH D 422 DISTANCE = 7.04 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 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 18 NE2 REMARK 620 2 HEC A 201 NA 88.7 REMARK 620 3 HEC A 201 NB 88.8 89.2 REMARK 620 4 HEC A 201 NC 91.3 179.6 90.4 REMARK 620 5 HEC A 201 ND 89.8 90.7 178.6 89.7 REMARK 620 6 MET A 80 SD 174.6 86.5 93.8 93.5 87.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC B 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 18 NE2 REMARK 620 2 HEC B 201 NA 89.6 REMARK 620 3 HEC B 201 NB 89.6 90.5 REMARK 620 4 HEC B 201 NC 90.6 179.3 88.9 REMARK 620 5 HEC B 201 ND 89.5 89.5 179.1 91.2 REMARK 620 6 MET B 80 SD 175.4 86.2 92.4 93.6 88.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC C 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 18 NE2 REMARK 620 2 HEC C 201 NA 89.3 REMARK 620 3 HEC C 201 NB 88.8 91.0 REMARK 620 4 HEC C 201 NC 91.7 178.9 88.6 REMARK 620 5 HEC C 201 ND 89.7 89.2 178.5 91.2 REMARK 620 6 MET C 80 SD 174.7 86.5 94.4 92.5 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 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 18 NE2 REMARK 620 2 HEC D 201 NA 90.5 REMARK 620 3 HEC D 201 NB 87.7 90.6 REMARK 620 4 HEC D 201 NC 90.1 179.1 88.8 REMARK 620 5 HEC D 201 ND 90.6 90.6 178.0 90.1 REMARK 620 6 MET D 80 SD 176.1 86.4 94.6 93.0 87.1 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FC6 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FC6 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FC6 B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FC6 C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide HEC B 201 and CYS B REMARK 800 14 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide HEC B 201 and CYS B REMARK 800 17 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide HEC C 201 and CYS C REMARK 800 17 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide HEC C 201 and CYS C REMARK 800 14 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide HEC D 201 and CYS D REMARK 800 17 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide HEC D 201 and CYS D REMARK 800 14 REMARK 999 REMARK 999 SEQUENCE REMARK 999 MOUSE CYTOCHROME C HAS THE SAME SEQUENCE (UNP P62897/CYC_MOUSE) AS REMARK 999 THIS ENTRY (UNP P62898/CYC_RAT) DBREF 5C0Z A 0 104 UNP P62898 CYC_RAT 1 105 DBREF 5C0Z B 0 104 UNP P62898 CYC_RAT 1 105 DBREF 5C0Z C 0 104 UNP P62898 CYC_RAT 1 105 DBREF 5C0Z D 0 104 UNP P62898 CYC_RAT 1 105 SEQRES 1 A 105 MET GLY ASP VAL GLU LYS GLY LYS LYS ILE PHE VAL GLN SEQRES 2 A 105 LYS CYS ALA GLN CYS HIS THR VAL GLU LYS GLY GLY LYS SEQRES 3 A 105 HIS LYS THR GLY PRO ASN LEU HIS GLY LEU PHE GLY ARG SEQRES 4 A 105 LYS THR GLY GLN ALA ALA GLY PHE SER TYR THR ASP ALA SEQRES 5 A 105 ASN LYS ASN LYS GLY ILE THR TRP GLY GLU ASP THR LEU SEQRES 6 A 105 MET GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY SEQRES 7 A 105 THR LYS MET ILE PHE ALA GLY ILE LYS LYS LYS GLY GLU SEQRES 8 A 105 ARG ALA ASP LEU ILE ALA TYR LEU LYS LYS ALA THR ASN SEQRES 9 A 105 GLU SEQRES 1 B 105 MET GLY ASP VAL GLU LYS GLY LYS LYS ILE PHE VAL GLN SEQRES 2 B 105 LYS CYS ALA GLN CYS HIS THR VAL GLU LYS GLY GLY LYS SEQRES 3 B 105 HIS LYS THR GLY PRO ASN LEU HIS GLY LEU PHE GLY ARG SEQRES 4 B 105 LYS THR GLY GLN ALA ALA GLY PHE SER TYR THR ASP ALA SEQRES 5 B 105 ASN LYS ASN LYS GLY ILE THR TRP GLY GLU ASP THR LEU SEQRES 6 B 105 MET GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY SEQRES 7 B 105 THR LYS MET ILE PHE ALA GLY ILE LYS LYS LYS GLY GLU SEQRES 8 B 105 ARG ALA ASP LEU ILE ALA TYR LEU LYS LYS ALA THR ASN SEQRES 9 B 105 GLU SEQRES 1 C 105 MET GLY ASP VAL GLU LYS GLY LYS LYS ILE PHE VAL GLN SEQRES 2 C 105 LYS CYS ALA GLN CYS HIS THR VAL GLU LYS GLY GLY LYS SEQRES 3 C 105 HIS LYS THR GLY PRO ASN LEU HIS GLY LEU PHE GLY ARG SEQRES 4 C 105 LYS THR GLY GLN ALA ALA GLY PHE SER TYR THR ASP ALA SEQRES 5 C 105 ASN LYS ASN LYS GLY ILE THR TRP GLY GLU ASP THR LEU SEQRES 6 C 105 MET GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY SEQRES 7 C 105 THR LYS MET ILE PHE ALA GLY ILE LYS LYS LYS GLY GLU SEQRES 8 C 105 ARG ALA ASP LEU ILE ALA TYR LEU LYS LYS ALA THR ASN SEQRES 9 C 105 GLU SEQRES 1 D 105 MET GLY ASP VAL GLU LYS GLY LYS LYS ILE PHE VAL GLN SEQRES 2 D 105 LYS CYS ALA GLN CYS HIS THR VAL GLU LYS GLY GLY LYS SEQRES 3 D 105 HIS LYS THR GLY PRO ASN LEU HIS GLY LEU PHE GLY ARG SEQRES 4 D 105 LYS THR GLY GLN ALA ALA GLY PHE SER TYR THR ASP ALA SEQRES 5 D 105 ASN LYS ASN LYS GLY ILE THR TRP GLY GLU ASP THR LEU SEQRES 6 D 105 MET GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY SEQRES 7 D 105 THR LYS MET ILE PHE ALA GLY ILE LYS LYS LYS GLY GLU SEQRES 8 D 105 ARG ALA ASP LEU ILE ALA TYR LEU LYS LYS ALA THR ASN SEQRES 9 D 105 GLU HET HEC A 201 43 HET FC6 A 202 26 HET HEC B 201 43 HET FC6 B 202 13 HET FC6 B 203 26 HET HEC C 201 43 HET FC6 C 202 13 HET HEC D 201 43 HETNAM HEC HEME C HETNAM FC6 HEXACYANOFERRATE(3-) HETSYN FC6 FERRI(III)HEXACYANIDE FORMUL 5 HEC 4(C34 H34 FE N4 O4) FORMUL 6 FC6 4(C6 FE N6) FORMUL 13 HOH *537(H2 O) HELIX 1 AA1 ASP A 2 CYS A 14 1 13 HELIX 2 AA2 THR A 49 LYS A 55 1 7 HELIX 3 AA3 GLY A 60 ASN A 70 1 11 HELIX 4 AA4 ASN A 70 ILE A 75 1 6 HELIX 5 AA5 LYS A 87 THR A 102 1 16 HELIX 6 AA6 ASP B 2 CYS B 14 1 13 HELIX 7 AA7 THR B 49 LYS B 55 1 7 HELIX 8 AA8 GLY B 60 ASN B 70 1 11 HELIX 9 AA9 ASN B 70 ILE B 75 1 6 HELIX 10 AB1 LYS B 87 THR B 102 1 16 HELIX 11 AB2 ASP C 2 CYS C 14 1 13 HELIX 12 AB3 THR C 49 LYS C 55 1 7 HELIX 13 AB4 GLY C 60 ASN C 70 1 11 HELIX 14 AB5 ASN C 70 ILE C 75 1 6 HELIX 15 AB6 LYS C 87 THR C 102 1 16 HELIX 16 AB7 ASP D 2 CYS D 14 1 13 HELIX 17 AB8 THR D 49 ASN D 54 1 6 HELIX 18 AB9 GLY D 60 ASN D 70 1 11 HELIX 19 AC1 ASN D 70 ILE D 75 1 6 HELIX 20 AC2 LYS D 87 THR D 102 1 16 LINK SG CYS A 14 CAB HEC A 201 1555 1555 1.86 LINK SG CYS A 17 CAC HEC A 201 1555 1555 1.98 LINK SG CYS B 14 CAB HEC B 201 1555 1555 1.86 LINK SG CYS B 17 CAC HEC B 201 1555 1555 1.94 LINK SG CYS C 14 CAB HEC C 201 1555 1555 1.91 LINK SG CYS C 17 CAC HEC C 201 1555 1555 1.97 LINK SG CYS D 14 CAB HEC D 201 1555 1555 1.95 LINK SG CYS D 17 CAC HEC D 201 1555 1555 2.04 LINK NE2 HIS A 18 FE HEC A 201 1555 1555 2.02 LINK SD MET A 80 FE HEC A 201 1555 1555 2.29 LINK NE2 HIS B 18 FE HEC B 201 1555 1555 2.03 LINK SD MET B 80 FE HEC B 201 1555 1555 2.28 LINK NE2 HIS C 18 FE HEC C 201 1555 1555 2.02 LINK SD MET C 80 FE HEC C 201 1555 1555 2.30 LINK NE2 HIS D 18 FE HEC D 201 1555 1555 2.02 LINK SD MET D 80 FE HEC D 201 1555 1555 2.31 SITE 1 AC1 20 LYS A 13 CYS A 14 CYS A 17 HIS A 18 SITE 2 AC1 20 THR A 28 GLY A 29 PRO A 30 THR A 40 SITE 3 AC1 20 GLY A 41 TYR A 48 THR A 49 ASN A 52 SITE 4 AC1 20 TRP A 59 TYR A 67 THR A 78 LYS A 79 SITE 5 AC1 20 MET A 80 ILE A 81 PHE A 82 HOH A 318 SITE 1 AC2 20 LYS A 13 GLY A 84 ILE A 85 LYS A 86 SITE 2 AC2 20 LYS A 87 HOH A 328 HOH A 334 HOH A 335 SITE 3 AC2 20 HOH A 345 LYS D 13 ILE D 85 LYS D 86 SITE 4 AC2 20 LYS D 87 HOH D 301 HOH D 302 HOH D 304 SITE 5 AC2 20 HOH D 307 HOH D 324 HOH D 332 HOH D 378 SITE 1 AC3 9 LYS A 87 LYS A 88 GLY A 89 GLU A 90 SITE 2 AC3 9 LYS B 87 LYS B 88 GLY B 89 GLU B 90 SITE 3 AC3 9 HOH B 308 SITE 1 AC4 16 LYS B 13 ILE B 85 LYS B 86 LYS B 87 SITE 2 AC4 16 HOH B 326 HOH B 336 LYS C 13 ILE C 85 SITE 3 AC4 16 LYS C 86 LYS C 87 HOH C 301 HOH C 302 SITE 4 AC4 16 HOH C 304 HOH C 325 HOH C 336 HOH C 357 SITE 1 AC5 14 LYS C 87 LYS C 88 GLY C 89 HOH C 348 SITE 2 AC5 14 HOH C 361 HOH C 365 HOH C 372 HOH C 396 SITE 3 AC5 14 HOH C 397 LYS D 87 LYS D 88 GLY D 89 SITE 4 AC5 14 HOH D 363 HOH D 420 SITE 1 AC6 22 PHE B 10 LYS B 13 ALA B 15 GLN B 16 SITE 2 AC6 22 CYS B 17 HIS B 18 THR B 28 GLY B 29 SITE 3 AC6 22 PRO B 30 THR B 40 GLY B 41 TYR B 48 SITE 4 AC6 22 THR B 49 ASN B 52 TRP B 59 TYR B 67 SITE 5 AC6 22 THR B 78 LYS B 79 MET B 80 PHE B 82 SITE 6 AC6 22 HOH B 311 HOH B 325 SITE 1 AC7 23 LYS B 13 CYS B 14 ALA B 15 GLN B 16 SITE 2 AC7 23 HIS B 18 LYS B 27 THR B 28 GLY B 29 SITE 3 AC7 23 PRO B 30 THR B 40 GLY B 41 TYR B 48 SITE 4 AC7 23 THR B 49 ASN B 52 TRP B 59 TYR B 67 SITE 5 AC7 23 THR B 78 LYS B 79 MET B 80 PHE B 82 SITE 6 AC7 23 HOH B 311 HOH B 325 ILE C 81 SITE 1 AC8 24 ILE B 81 LYS C 13 CYS C 14 ALA C 15 SITE 2 AC8 24 GLN C 16 HIS C 18 LYS C 27 THR C 28 SITE 3 AC8 24 GLY C 29 PRO C 30 THR C 40 GLY C 41 SITE 4 AC8 24 TYR C 48 THR C 49 ASN C 52 TRP C 59 SITE 5 AC8 24 TYR C 67 THR C 78 LYS C 79 MET C 80 SITE 6 AC8 24 ILE C 81 PHE C 82 HOH C 323 HOH C 367 SITE 1 AC9 23 PHE C 10 LYS C 13 ALA C 15 GLN C 16 SITE 2 AC9 23 CYS C 17 HIS C 18 THR C 28 GLY C 29 SITE 3 AC9 23 PRO C 30 THR C 40 GLY C 41 TYR C 48 SITE 4 AC9 23 THR C 49 ASN C 52 TRP C 59 TYR C 67 SITE 5 AC9 23 THR C 78 LYS C 79 MET C 80 ILE C 81 SITE 6 AC9 23 PHE C 82 HOH C 323 HOH C 367 SITE 1 AD1 24 ILE A 81 LYS D 13 CYS D 14 ALA D 15 SITE 2 AD1 24 GLN D 16 HIS D 18 LYS D 27 THR D 28 SITE 3 AD1 24 GLY D 29 PRO D 30 THR D 40 GLY D 41 SITE 4 AD1 24 TYR D 48 THR D 49 ASN D 52 TRP D 59 SITE 5 AD1 24 TYR D 67 THR D 78 LYS D 79 MET D 80 SITE 6 AD1 24 ILE D 81 PHE D 82 HOH D 325 HOH D 336 SITE 1 AD2 22 PHE D 10 LYS D 13 ALA D 15 GLN D 16 SITE 2 AD2 22 CYS D 17 HIS D 18 THR D 28 PRO D 30 SITE 3 AD2 22 THR D 40 GLY D 41 TYR D 48 THR D 49 SITE 4 AD2 22 ASN D 52 TRP D 59 TYR D 67 THR D 78 SITE 5 AD2 22 LYS D 79 MET D 80 ILE D 81 PHE D 82 SITE 6 AD2 22 HOH D 325 HOH D 336 CRYST1 34.401 52.471 61.647 110.04 92.77 92.02 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 0.029069 0.001026 0.001878 0.00000 SCALE2 0.000000 0.019070 0.007008 0.00000 SCALE3 0.000000 0.000000 0.017302 0.00000