HEADER ELECTRON TRANSPORT 07-NOV-96 1B5M TITLE RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME B5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WATER SOLUBLE DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: FROM RAT OUTER MITOCHONDRIAL MEMBRANE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 CELL_LINE: BL21; SOURCE 6 ORGAN: LIVER; SOURCE 7 CELL: HEPATOCYTE; SOURCE 8 ORGANELLE: MITOCHONDRION; SOURCE 9 CELLULAR_LOCATION: OUTER MITOCHONDRIAL MEMBRANE; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 13 EXPRESSION_SYSTEM_CELLULAR_LOCATION: PERIPLASMIC SPACE; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PET 11A KEYWDS CYTOCHROME, ELECTRON TRANSPORT, HEME EXPDTA X-RAY DIFFRACTION AUTHOR M.RIVERA,S.P.WHITE,X.ZHANG REVDAT 5 22-MAY-24 1B5M 1 REMARK REVDAT 4 02-AUG-23 1B5M 1 REMARK LINK REVDAT 3 24-FEB-09 1B5M 1 VERSN REVDAT 2 01-APR-03 1B5M 1 JRNL REVDAT 1 12-MAR-97 1B5M 0 JRNL AUTH M.J.RODRIGUEZ-MARANON,F.QIU,R.E.STARK,S.P.WHITE,X.ZHANG, JRNL AUTH 2 S.I.FOUNDLING,V.RODRIGUEZ,C.L.SCHILLING 3RD.,R.A.BUNCE, JRNL AUTH 3 M.RIVERA JRNL TITL 13C NMR SPECTROSCOPIC AND X-RAY CRYSTALLOGRAPHIC STUDY OF JRNL TITL 2 THE ROLE PLAYED BY MITOCHONDRIAL CYTOCHROME B5 HEME JRNL TITL 3 PROPIONATES IN THE ELECTROSTATIC BINDING TO CYTOCHROME C. JRNL REF BIOCHEMISTRY V. 35 16378 1996 JRNL REFN ISSN 0006-2960 JRNL PMID 8973214 JRNL DOI 10.1021/BI961895O REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5E REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 3123 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3123 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.2200 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 3123 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 676 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 36.000 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.016 ; 0.800 ; 744 REMARK 3 BOND ANGLES (DEGREES) : 2.900 ; 1.300 ; 1003 REMARK 3 TORSION ANGLES (DEGREES) : 20.000; 0.000 ; 412 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.007 ; 2.000 ; 23 REMARK 3 GENERAL PLANES (A) : 0.012 ; 5.000 ; 104 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 4.990 ; 2.000 ; 692 REMARK 3 NON-BONDED CONTACTS (A) : 0.023 ; 10.000; 25 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : BSOL REMARK 3 KSOL : 0.79 REMARK 3 BSOL : 99.70 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B5M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171491. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-96 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : DIAMOND C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : FRAMBO, SADIE REMARK 200 DATA SCALING SOFTWARE : SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3123 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 1.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.08800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MRCHK REMARK 200 STARTING MODEL: PDB ENTRY 3B5C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED BY VAPOR REMARK 280 DIFFUSION TOGETHER WITH SLOW EVAPORATION USING 20% PEG 8000 IN REMARK 280 0.1M SODIUM CACODYLATE (PH = 6.5 WITH 0.2 M MAGNESIUM ACETATE., REMARK 280 VAPOR DIFFUSION WITH SLOW EVAPORATION, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 109.50000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 15.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 15.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 164.25000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 15.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 15.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.75000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 15.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 15.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 164.25000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 15.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 15.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.75000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 109.50000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 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 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 19 CD GLU A 19 OE2 0.067 REMARK 500 GLU A 20 CD GLU A 20 OE2 0.072 REMARK 500 GLU A 43 CD GLU A 43 OE2 0.071 REMARK 500 GLU A 44 CD GLU A 44 OE2 0.096 REMARK 500 GLU A 59 CD GLU A 59 OE1 0.070 REMARK 500 GLU A 69 CD GLU A 69 OE2 0.074 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 15 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 31 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 SER A 57 CB - CA - C ANGL. DEV. = 12.8 DEGREES REMARK 500 ASP A 60 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 66 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 TYR A 75 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP A 83 CB - CG - OD1 ANGL. DEV. = 8.4 DEGREES REMARK 500 ASP A 83 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 PRO A 86 C - N - CD ANGL. DEV. = -44.5 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 ARG A 15 44.97 -89.12 REMARK 500 THR A 33 -59.24 -29.56 REMARK 500 LEU A 36 -51.53 -21.77 REMARK 500 HIS A 39 106.06 -51.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 39 NE2 REMARK 620 2 HEM A 201 NA 85.7 REMARK 620 3 HEM A 201 NB 98.9 88.6 REMARK 620 4 HEM A 201 NC 99.1 175.2 91.2 REMARK 620 5 HEM A 201 ND 90.9 89.6 169.9 89.7 REMARK 620 6 HIS A 63 NE2 166.3 98.0 94.4 77.2 76.0 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 HEM A 201 DBREF 1B5M A 3 86 UNP P04166 CYM5_RAT 19 102 SEQRES 1 A 84 ALA VAL THR TYR TYR ARG LEU GLU GLU VAL ALA LYS ARG SEQRES 2 A 84 ASN THR ALA GLU GLU THR TRP MET VAL ILE HIS GLY ARG SEQRES 3 A 84 VAL TYR ASP ILE THR ARG PHE LEU SER GLU HIS PRO GLY SEQRES 4 A 84 GLY GLU GLU VAL LEU LEU GLU GLN ALA GLY ALA ASP ALA SEQRES 5 A 84 THR GLU SER PHE GLU ASP VAL GLY HIS SER PRO ASP ALA SEQRES 6 A 84 ARG GLU MET LEU LYS GLN TYR TYR ILE GLY ASP VAL HIS SEQRES 7 A 84 PRO ASN ASP LEU LYS PRO HET HEM A 201 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 HELIX 1 1 LEU A 9 LYS A 14 1 6 HELIX 2 2 GLU A 44 GLN A 49 1 6 HELIX 3 3 THR A 55 VAL A 61 1 7 HELIX 4 4 PRO A 65 GLN A 73 1 9 SHEET 1 A 3 TRP A 22 ILE A 25 0 SHEET 2 A 3 ARG A 28 ASP A 31 -1 N TYR A 30 O MET A 23 SHEET 3 A 3 TYR A 75 ASP A 78 -1 N GLY A 77 O VAL A 29 LINK NE2 HIS A 39 FE HEM A 201 1555 1555 1.92 LINK NE2 HIS A 63 FE HEM A 201 1555 1555 1.82 SITE 1 AC1 16 PHE A 35 HIS A 39 PRO A 40 GLY A 41 SITE 2 AC1 16 GLU A 44 LEU A 46 GLN A 49 ALA A 54 SITE 3 AC1 16 SER A 57 PHE A 58 VAL A 61 HIS A 63 SITE 4 AC1 16 SER A 64 ALA A 67 ARG A 68 LEU A 71 CRYST1 30.000 30.000 219.000 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.033333 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004566 0.00000