HEADER ELECTRON TRANSPORT 01-AUG-76 155C TITLE THE STRUCTURE OF PARACOCCUS DENITRIFICANS CYTOCHROME C550 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C550; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARACOCCUS DENITRIFICANS; SOURCE 3 ORGANISM_COMMON: MICROCOCCUS DENITRIFICANS; SOURCE 4 ORGANISM_TAXID: 266 KEYWDS ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR R.TIMKOVICH REVDAT 13 16-OCT-24 155C 1 REMARK REVDAT 12 05-JUN-24 155C 1 REMARK SEQADV LINK REVDAT 11 25-AUG-09 155C 1 SOURCE REVDAT 10 24-FEB-09 155C 1 VERSN REVDAT 9 15-OCT-91 155C 1 JRNL REVDAT 8 30-SEP-83 155C 1 REVDAT REVDAT 7 25-OCT-82 155C 3 SEQRES FTNOTE ATOM REVDAT 6 31-DEC-80 155C 1 REMARK REVDAT 5 05-MAR-80 155C 1 SOURCE REVDAT 4 19-SEP-78 155C 2 CONECT REVDAT 3 20-JUL-78 155C 2 CONECT REVDAT 2 01-NOV-77 155C 1 SOURCE AUTHOR JRNL REMARK REVDAT 2 2 1 FORMUL REVDAT 1 20-AUG-76 155C 0 JRNL AUTH R.TIMKOVICH,R.E.DICKERSON JRNL TITL THE STRUCTURE OF PARACOCCUS DENITRIFICANS CYTOCHROME C550. JRNL REF J.BIOL.CHEM. V. 251 4033 1976 JRNL REFN ISSN 0021-9258 JRNL PMID 180013 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.TIMKOVICH,R.E.DICKERSON,E.MARGOLIASH REMARK 1 TITL AMINO ACID SEQUENCE OF PARACOCCUS DENITRIFICANS CYTOCHROME REMARK 1 TITL 2 C550 REMARK 1 REF J.BIOL.CHEM. V. 251 2197 1976 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 EDIT R.J.FELDMANN REMARK 1 REF ATLAS OF MACROMOLECULAR 115 1976 REMARK 1 REF 2 STRUCTURE ON MICROFICHE REMARK 1 PUBL TRACOR JITCO INC.,ROCKVILLE,MD. REMARK 1 REFN REMARK 1 REFERENCE 3 REMARK 1 EDIT M.O.DAYHOFF REMARK 1 REF ATLAS OF PROTEIN SEQUENCE V. 5 45 1976 REMARK 1 REF 2 AND STRUCTURE,SUPPLEMENT 2 REMARK 1 PUBL NATIONAL BIOMEDICAL RESEARCH FOUNDATION, SILVER SPRING,MD. REMARK 1 REFN ISSN 0-912466-05-7 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 974 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 155C 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_1000170126. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 21.35000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.78000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.08500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 15.78000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.35000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.08500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 135 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 19 NE2 REMARK 620 2 HEM A 135 NA 86.2 REMARK 620 3 HEM A 135 NB 89.9 88.0 REMARK 620 4 HEM A 135 NC 89.7 175.7 91.0 REMARK 620 5 HEM A 135 ND 88.3 89.0 176.6 91.8 REMARK 620 6 MET A 99 SD 179.7 94.1 89.9 90.1 91.9 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 135 REMARK 999 REMARK 999 SEQUENCE REMARK 999 SIDE CHAIN ATOMS FOR RESIDUES 122 TO 134 ARE NOT INCLUDED BECAUSE REMARK 999 THE SEQUENCE IN THIS REGION IS NOT DEFINITIVELY KNOWN. THE RESIDUES REMARK 999 HAVE BEEN LABELLED AS UNK. DBREF 155C A 3 121 UNP P00096 C550_PARDE 23 142 SEQADV 155C A UNP P00096 ILE 49 DELETION SEQADV 155C ASN A 74 UNP P00096 ASP 95 CONFLICT SEQADV 155C LEU A 85 UNP P00096 TRP 106 CONFLICT SEQADV 155C VAL A 86 UNP P00096 LEU 107 CONFLICT SEQADV 155C LYS A 87 UNP P00096 VAL 108 CONFLICT SEQADV 155C ASP A 117 UNP P00096 ASN 138 CONFLICT SEQADV 155C ASP A 118 UNP P00096 SER 139 CONFLICT SEQRES 1 A 135 ACE ASN GLU GLY ASP ALA ALA LYS GLY GLU LYS GLU PHE SEQRES 2 A 135 ASN LYS CYS LYS ALA CYS HIS MET ILE GLN ALA PRO ASP SEQRES 3 A 135 GLY THR ASP ILE LYS GLY GLY LYS THR GLY PRO ASN LEU SEQRES 4 A 135 TYR GLY VAL VAL GLY ARG LYS ILE ALA SER GLU GLU GLY SEQRES 5 A 135 PHE LYS TYR GLY GLU GLY ILE LEU GLU VAL ALA GLU LYS SEQRES 6 A 135 ASN PRO ASP LEU THR TRP THR GLU ALA ASN LEU ILE GLU SEQRES 7 A 135 TYR VAL THR ASP PRO LYS PRO LEU VAL LYS LYS MET THR SEQRES 8 A 135 ASP ASP LYS GLY ALA LYS THR LYS MET THR PHE LYS MET SEQRES 9 A 135 GLY LYS ASN GLN ALA ASP VAL VAL ALA PHE LEU ALA GLN SEQRES 10 A 135 ASP ASP PRO ASP ALA UNK UNK UNK UNK UNK UNK UNK UNK SEQRES 11 A 135 UNK UNK UNK UNK UNK HET ACE A 0 3 HET HEM A 135 43 HETNAM ACE ACETYL GROUP HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 1 ACE C2 H4 O FORMUL 2 HEM C34 H32 FE N4 O4 HELIX 1 1 ALA A 5 ASN A 13 1 9 HELIX 2 2 GLY A 55 ASN A 65 1 11 HELIX 3 3 GLU A 72 ASP A 81 1 10 HELIX 4 4 ASN A 106 ASP A 118 1 13 SHEET 1 A 2 HIS A 19 MET A 20 0 SHEET 2 A 2 GLY A 35 ASN A 37 1 O GLY A 35 N MET A 20 LINK C ACE A 0 N ASN A 1 1555 1555 1.13 LINK NE2 HIS A 19 FE HEM A 135 1555 1555 2.26 LINK SD MET A 99 FE HEM A 135 1555 1555 2.16 SITE 1 AC1 15 CYS A 15 CYS A 18 HIS A 19 ILE A 46 SITE 2 AC1 15 ALA A 47 TYR A 54 GLY A 55 ILE A 58 SITE 3 AC1 15 TRP A 70 TYR A 78 VAL A 79 PRO A 84 SITE 4 AC1 15 LYS A 98 MET A 99 PHE A 101 CRYST1 42.700 82.170 31.560 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 0.023419 0.000000 0.000000 0.00000 ORIGX2 0.000000 0.012170 0.000000 0.00000 ORIGX3 0.000000 0.000000 0.031686 0.00000 SCALE1 0.023419 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012170 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031686 0.00000 HETATM 1 C ACE A 0 -4.041 34.746 22.832 1.00 0.00 C HETATM 2 O ACE A 0 -3.132 35.608 23.027 1.00 0.00 O HETATM 3 CH3 ACE A 0 -5.385 35.202 22.167 1.00 0.00 C