HEADER ELECTRON TRANSPORT 05-APR-12 4EIC TITLE CRYSTAL STRUCTURE OF REDUCED CYTOCHROME C6 FROM SYNECHOCOCCUS SP. PCC TITLE 2 7002 AT ULTRA-HIGH RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 25-117; COMPND 5 SYNONYM: CYTOCHROME C-553, CYTOCHROME C553, SOLUBLE CYTOCHROME F; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS SP.; SOURCE 3 ORGANISM_TAXID: 32049; SOURCE 4 STRAIN: ATCC 27264 / PCC 7002 / PR-6; SOURCE 5 GENE: PETJ, PETJ1, SYNPCC7002_A0167; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 668369; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH5A; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PUCJ1; SOURCE 11 OTHER_DETAILS: CO-EXPRESSION WITH PEC86 KEYWDS ELECTRON TRANSPORT, CYTOCHROME C6 EXPDTA X-RAY DIFFRACTION AUTHOR S.KRZYWDA,W.BIALEK,M.JASKOLSKI,A.SZCZEPANIAK REVDAT 3 13-SEP-23 4EIC 1 REMARK REVDAT 2 10-MAR-21 4EIC 1 COMPND REMARK HET HETNAM REVDAT 2 2 1 HETSYN FORMUL LINK ATOM REVDAT 1 10-APR-13 4EIC 0 JRNL AUTH W.BIALEK,S.KRZYWDA,P.ZATWARNICKI,M.JASKOLSKI,A.SZCZEPANIAK JRNL TITL CYTOCHROME C6 AND C6C FROM SYNECHOCOCCUS SP. PCC 7002 - JRNL TITL 2 STRUCTURE AND FUNCTION. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.BIALEK,S.KRZYWDA,M.JASKOLSKI,A.SZCZEPANIAK REMARK 1 TITL ATOMIC-RESOLUTION STRUCTURE OF REDUCED CYANOBACTERIAL REMARK 1 TITL 2 CYTOCHROME C6 WITH AN UNUSUAL SEQUENCE INSERTION. REMARK 1 REF FEBS J. V. 276 4426 2009 REMARK 1 REFN ISSN 1742-464X REMARK 1 PMID 19678839 REMARK 1 DOI 10.1111/J.1742-4658.2009.07150.X REMARK 1 REFERENCE 2 REMARK 1 AUTH W.BIALEK,M.NELSON,K.TAMIOLA,T.KALLAS,A.SZCZEPANIAK REMARK 1 TITL DEEPLY BRANCHING C6-LIKE CYTOCHROMES OF CYANOBACTERIA. REMARK 1 REF BIOCHEMISTRY V. 47 5515 2008 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 18439023 REMARK 1 DOI 10.1021/BI701973G REMARK 2 REMARK 2 RESOLUTION. 0.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.106 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.106 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.127 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 1.500 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 974 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 64908 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.095 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.095 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.118 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 1.500 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 823 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 54437 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 662 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 800.71 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 664.26 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 12 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7849 REMARK 3 NUMBER OF RESTRAINTS : 7790 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.026 REMARK 3 ANGLE DISTANCES (A) : 0.057 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.004 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.115 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.093 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.025 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.080 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT, HYDROGENS HAVE REMARK 3 BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 4EIC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071654. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8166 REMARK 200 MONOCHROMATOR : GE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64908 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.840 REMARK 200 RESOLUTION RANGE LOW (A) : 32.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.50700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.230 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3DR0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M AMMONIUM SULPHATE, 0.1M MES, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 13.84500 REMARK 290 SMTRY3 2 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 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 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 101 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 18 NE2 REMARK 620 2 HEC A 101 NA 91.1 REMARK 620 3 HEC A 101 NB 90.0 90.2 REMARK 620 4 HEC A 101 NC 88.7 179.6 90.1 REMARK 620 5 HEC A 101 ND 90.6 89.9 179.3 89.7 REMARK 620 6 MET A 65 SD 175.4 84.6 91.6 95.6 87.8 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DR0 RELATED DB: PDB REMARK 900 THE SAME PROTEIN AT 1.23 A RESOLUTION REMARK 900 RELATED ID: 4EID RELATED DB: PDB REMARK 900 RELATED ID: 4EIE RELATED DB: PDB REMARK 900 RELATED ID: 4EIF RELATED DB: PDB DBREF 4EIC A 1 93 UNP O30881 CYC6_SYNP2 25 117 SEQRES 1 A 93 ALA ASP ALA ALA ALA GLY ALA GLN VAL PHE ALA ALA ASN SEQRES 2 A 93 CYS ALA ALA CYS HIS ALA GLY GLY ASN ASN ALA VAL MET SEQRES 3 A 93 PRO THR LYS THR LEU LYS ALA ASP ALA LEU LYS THR TYR SEQRES 4 A 93 LEU ALA GLY TYR LYS ASP GLY SER LYS SER LEU GLU GLU SEQRES 5 A 93 ALA VAL ALA TYR GLN VAL THR ASN GLY GLN GLY ALA MET SEQRES 6 A 93 PRO ALA PHE GLY GLY ARG LEU SER ASP ALA ASP ILE ALA SEQRES 7 A 93 ASN VAL ALA ALA TYR ILE ALA ASP GLN ALA GLU ASN ASN SEQRES 8 A 93 LYS TRP HET HEC A 101 43 HET MES A 102 12 HETNAM HEC HEME C HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 2 HEC C34 H34 FE N4 O4 FORMUL 3 MES C6 H13 N O4 S FORMUL 4 HOH *120(H2 O) HELIX 1 1 ASP A 2 CYS A 14 1 13 HELIX 2 2 CYS A 14 ALA A 19 1 6 HELIX 3 3 GLY A 20 ASN A 22 5 3 HELIX 4 4 LYS A 32 LEU A 40 1 9 HELIX 5 5 SER A 49 GLY A 61 1 13 HELIX 6 6 SER A 73 ASN A 90 1 18 LINK SG CYS A 14 CAB HEC A 101 1555 1555 1.83 LINK SG CYS A 17 CAC HEC A 101 1555 1555 1.84 LINK NE2 HIS A 18 FE HEC A 101 1555 1555 1.98 LINK SD MET A 65 FE HEC A 101 1555 1555 2.34 SITE 1 AC1 20 ASN A 13 CYS A 14 CYS A 17 HIS A 18 SITE 2 AC1 20 ASN A 23 VAL A 25 MET A 26 LYS A 29 SITE 3 AC1 20 THR A 30 LEU A 31 ALA A 35 TYR A 39 SITE 4 AC1 20 LEU A 40 GLN A 57 VAL A 58 GLN A 62 SITE 5 AC1 20 MET A 65 HOH A 201 HOH A 215 HOH A 268 SITE 1 AC2 1 CYS A 17 CRYST1 31.860 27.690 44.070 90.00 101.10 90.00 P 1 21 1 2 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 0.031387 0.000000 0.006128 0.00000 SCALE2 0.000000 0.036114 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023120 0.00000