HEADER ELECTRON TRANSPORT 28-JUN-15 5C9M TITLE THE STRUCTURE OF OXIDIZED RAT CYTOCHROME C (T28A) AT 1.362 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; COMPND 5 MUTATION: 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 C OXIDIZED RAT MUTANT, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR B.F.P.EDWARDS,G.MAHAPATRA,A.A.VAISHNAV,J.S.BRUNZELLE,M.HUTTEMANN REVDAT 6 23-OCT-24 5C9M 1 REMARK REVDAT 5 27-SEP-23 5C9M 1 LINK REVDAT 4 25-DEC-19 5C9M 1 LINK REVDAT 3 01-NOV-17 5C9M 1 REMARK REVDAT 2 06-SEP-17 5C9M 1 REMARK REVDAT 1 21-SEP-16 5C9M 0 JRNL AUTH B.F.P.EDWARDS,G.MAHAPATRA,A.A.VAISHNAV,J.S.BRUNZELLE, JRNL AUTH 2 M.HUTTEMANN JRNL TITL THE STRUCTURE OF OXIDIZED RAT CYTOCHROME C (T28A) AT 1.362 JRNL TITL 2 ANGSTROMS RESOLUTION. JRNL REF TO BE PUBLISHED JRNL REFN 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. 1.36 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) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 76544 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) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.129 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 3901 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) : 1.36 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4056 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 202 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3220 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 224 REMARK 3 SOLVENT ATOMS : 472 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : -0.51000 REMARK 3 B33 (A**2) : -0.22000 REMARK 3 B12 (A**2) : 0.04000 REMARK 3 B13 (A**2) : 0.89000 REMARK 3 B23 (A**2) : 0.85000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.057 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.055 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.039 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.244 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3552 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3380 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4826 ; 1.803 ; 2.063 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7812 ; 1.058 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 412 ; 6.497 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 132 ;31.917 ;25.152 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 648 ;12.075 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;31.575 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 456 ; 0.122 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3928 ; 0.015 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 792 ; 0.014 ; 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): 1660 ; 1.482 ; 1.807 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1659 ; 1.482 ; 1.806 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2068 ; 1.824 ; 2.720 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2069 ; 1.824 ; 2.721 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1892 ; 2.042 ; 2.063 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1818 ; 2.033 ; 2.060 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2632 ; 2.450 ; 2.923 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4679 ; 3.725 ;16.186 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4441 ; 3.046 ;15.291 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6932 ; 2.519 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 137 ;35.915 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7187 ;12.158 ; 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 : 1.00 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 5C9M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000211221. 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 : 6.5-7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : DIAMOND LAUE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JAN. 10, 2014 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76544 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.362 REMARK 200 RESOLUTION RANGE LOW (A) : 57.962 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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: 5C0Z REMARK 200 REMARK 200 REMARK: 0.3 X0.1 MM PRISMS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MG/ML PROTEIN, PEG 4000, REMARK 280 ISOPROPANOL, SODIUM ACETATE, POTASSIUM FERRICYANATE, PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, 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 300 REMARK: MONOMER CONFIRMED BY GEL FILTRATION 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 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 - NH2 ANGL. DEV. = -3.5 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 -135.72 -127.35 REMARK 500 ASN A 70 83.36 -167.90 REMARK 500 LYS B 27 -136.33 -124.70 REMARK 500 ASN B 70 89.83 -165.12 REMARK 500 LYS C 27 -135.68 -122.43 REMARK 500 ASN C 70 87.68 -163.57 REMARK 500 LYS D 27 -135.40 -124.53 REMARK 500 ASN D 70 89.86 -165.54 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 B 424 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH C 419 DISTANCE = 6.69 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 89.4 REMARK 620 3 HEC A 201 NB 87.9 89.6 REMARK 620 4 HEC A 201 NC 90.4 179.6 90.0 REMARK 620 5 HEC A 201 ND 90.5 90.5 178.4 89.9 REMARK 620 6 MET A 80 SD 175.5 86.4 93.8 93.8 87.8 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 90.2 REMARK 620 3 HEC B 201 NB 88.3 89.2 REMARK 620 4 HEC B 201 NC 90.5 178.9 90.0 REMARK 620 5 HEC B 201 ND 90.3 91.3 178.5 89.6 REMARK 620 6 MET B 80 SD 176.1 86.0 92.6 93.3 88.9 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 89.7 REMARK 620 3 HEC C 201 NB 87.4 89.5 REMARK 620 4 HEC C 201 NC 90.0 179.2 89.7 REMARK 620 5 HEC C 201 ND 91.1 90.5 178.5 90.3 REMARK 620 6 MET C 80 SD 176.9 87.2 93.3 93.0 88.2 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 89.8 REMARK 620 3 HEC D 201 NB 88.0 89.4 REMARK 620 4 HEC D 201 NC 89.1 178.8 90.0 REMARK 620 5 HEC D 201 ND 90.7 90.6 178.7 89.9 REMARK 620 6 MET D 80 SD 177.6 88.0 93.1 93.1 88.3 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 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 HEC B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FC6 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FC6 B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEC C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FC6 C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEC D 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5C0Z RELATED DB: PDB REMARK 900 5C0Z CONTAINS THE NATIVE STRUCTURE OF RAT CYTOCHROME C 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 5C9M A 0 104 UNP P62898 CYC_RAT 1 105 DBREF 5C9M B 0 104 UNP P62898 CYC_RAT 1 105 DBREF 5C9M C 0 104 UNP P62898 CYC_RAT 1 105 DBREF 5C9M D 0 104 UNP P62898 CYC_RAT 1 105 SEQADV 5C9M ALA A 28 UNP P62898 THR 29 ENGINEERED MUTATION SEQADV 5C9M ALA B 28 UNP P62898 THR 29 ENGINEERED MUTATION SEQADV 5C9M ALA C 28 UNP P62898 THR 29 ENGINEERED MUTATION SEQADV 5C9M ALA D 28 UNP P62898 THR 29 ENGINEERED MUTATION 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 ALA 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 ALA 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 ALA 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 ALA 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 *472(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 LYS D 55 1 7 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 1.92 LINK SG CYS A 17 CAC HEC A 201 1555 1555 2.09 LINK SG CYS B 14 CAB HEC B 201 1555 1555 1.93 LINK SG CYS B 17 CAC HEC B 201 1555 1555 2.07 LINK SG CYS C 14 CAB HEC C 201 1555 1555 1.95 LINK SG CYS C 17 CAC HEC C 201 1555 1555 2.12 LINK SG CYS D 14 CAB HEC D 201 1555 1555 2.02 LINK SG CYS D 17 CAC HEC D 201 1555 1555 2.21 LINK NE2 HIS A 18 FE HEC A 201 1555 1555 2.03 LINK SD MET A 80 FE HEC A 201 1555 1555 2.27 LINK NE2 HIS B 18 FE HEC B 201 1555 1555 2.00 LINK SD MET B 80 FE HEC B 201 1555 1555 2.28 LINK NE2 HIS C 18 FE HEC C 201 1555 1555 2.04 LINK SD MET C 80 FE HEC C 201 1555 1555 2.28 LINK NE2 HIS D 18 FE HEC D 201 1555 1555 2.07 LINK SD MET D 80 FE HEC D 201 1555 1555 2.27 SITE 1 AC1 20 LYS A 13 CYS A 14 CYS A 17 HIS A 18 SITE 2 AC1 20 ALA 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 317 SITE 1 AC2 17 LYS A 13 GLY A 84 ILE A 85 LYS A 86 SITE 2 AC2 17 LYS A 87 HOH A 305 HOH A 321 HOH A 327 SITE 3 AC2 17 HOH A 333 LYS D 13 GLY D 84 ILE D 85 SITE 4 AC2 17 LYS D 86 LYS D 87 HOH D 327 HOH D 350 SITE 5 AC2 17 HOH D 355 SITE 1 AC3 21 LYS B 13 CYS B 14 CYS B 17 HIS B 18 SITE 2 AC3 21 ALA B 28 GLY B 29 PRO B 30 THR B 40 SITE 3 AC3 21 GLY B 41 TYR B 48 THR B 49 ASN B 52 SITE 4 AC3 21 TRP B 59 TYR B 67 LEU B 68 THR B 78 SITE 5 AC3 21 LYS B 79 MET B 80 ILE B 81 HOH B 314 SITE 6 AC3 21 HOH B 325 SITE 1 AC4 10 LYS A 87 LYS A 88 GLY A 89 GLU A 90 SITE 2 AC4 10 HOH A 404 LYS B 87 LYS B 88 GLY B 89 SITE 3 AC4 10 GLU B 90 HOH B 358 SITE 1 AC5 16 LYS B 13 GLY B 84 ILE B 85 LYS B 86 SITE 2 AC5 16 LYS B 87 HOH B 301 HOH B 303 HOH B 306 SITE 3 AC5 16 HOH B 328 HOH B 335 HOH B 385 LYS C 13 SITE 4 AC5 16 ILE C 85 LYS C 86 LYS C 87 HOH C 314 SITE 1 AC6 21 LYS C 13 CYS C 14 CYS C 17 HIS C 18 SITE 2 AC6 21 ALA C 28 GLY C 29 PRO C 30 THR C 40 SITE 3 AC6 21 GLY C 41 TYR C 48 THR C 49 ASN C 52 SITE 4 AC6 21 TRP C 59 TYR C 67 LEU C 68 THR C 78 SITE 5 AC6 21 LYS C 79 MET C 80 ILE C 81 HOH C 327 SITE 6 AC6 21 HOH C 340 SITE 1 AC7 9 LYS C 87 LYS C 88 GLY C 89 HOH C 358 SITE 2 AC7 9 HOH C 379 LYS D 87 LYS D 88 GLY D 89 SITE 3 AC7 9 HOH D 377 SITE 1 AC8 22 LYS D 13 CYS D 14 CYS D 17 HIS D 18 SITE 2 AC8 22 ALA D 28 GLY D 29 PRO D 30 THR D 40 SITE 3 AC8 22 GLY D 41 TYR D 48 THR D 49 ASN D 52 SITE 4 AC8 22 TRP D 59 TYR D 67 LEU D 68 THR D 78 SITE 5 AC8 22 LYS D 79 MET D 80 ILE D 81 PHE D 82 SITE 6 AC8 22 HOH D 318 HOH D 321 CRYST1 34.517 52.567 61.771 109.86 92.93 92.20 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 0.028971 0.001115 0.001982 0.00000 SCALE2 0.000000 0.019037 0.006937 0.00000 SCALE3 0.000000 0.000000 0.017253 0.00000