HEADER ELECTRON TRANSPORT 05-APR-12 4EID TITLE CRYSTAL STRUCTURE OF CYTOCHROME C6 Q57V MUTANT FROM SYNECHOCOCCUS SP. TITLE 2 PCC 7002 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; COMPND 7 MUTATION: 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 CYTOCHROME C6, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.KRZYWDA,W.BIALEK,P.ZATWARNICKI,M.JASKOLSKI,A.SZCZEPANIAK REVDAT 5 30-OCT-24 4EID 1 REMARK REVDAT 4 13-SEP-23 4EID 1 REMARK REVDAT 3 10-MAR-21 4EID 1 COMPND REMARK SEQADV HET REVDAT 3 2 1 HETNAM HETSYN FORMUL LINK REVDAT 3 3 1 ATOM REVDAT 2 27-SEP-17 4EID 1 REMARK REVDAT 1 10-APR-13 4EID 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. 1.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 27159 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) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.500 REMARK 3 FREE R VALUE TEST SET COUNT : 986 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) : 1.13 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1941 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 660 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.18000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : 0.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.85000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.034 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.036 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.024 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.177 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 755 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 457 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1037 ; 1.872 ; 2.131 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1122 ; 1.244 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 96 ; 5.598 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 30 ;39.816 ;26.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 102 ;10.140 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 1 ;20.177 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 105 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 867 ; 0.016 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 130 ; 0.009 ; 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): 465 ; 1.800 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 195 ; 0.872 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 727 ; 2.364 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 290 ; 3.356 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 309 ; 4.272 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1212 ; 1.528 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4EID 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_1000071655. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-10 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR555 FLAT PANEL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28144 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.130 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.45100 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3DR0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.03 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 13.81850 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 92.3 REMARK 620 3 HEC A 101 NB 89.3 89.5 REMARK 620 4 HEC A 101 NC 88.6 179.0 91.0 REMARK 620 5 HEC A 101 ND 90.9 90.2 179.6 89.3 REMARK 620 6 MET A 65 SD 176.5 84.3 91.8 94.7 87.9 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 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 RELATED ID: 4EIC RELATED DB: PDB REMARK 900 RELATED ID: 4EIE RELATED DB: PDB REMARK 900 RELATED ID: 4EIF RELATED DB: PDB DBREF 4EID A 1 93 UNP O30881 CYC6_SYNP2 25 117 SEQADV 4EID VAL A 57 UNP O30881 GLN 81 ENGINEERED MUTATION 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 VAL 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 *140(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 1.92 LINK NE2 HIS A 18 FE HEC A 101 1555 1555 2.00 LINK SD MET A 65 FE HEC A 101 1555 1555 2.33 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 VAL A 58 GLN A 62 MET A 65 SITE 5 AC1 20 PHE A 68 HOH A 216 HOH A 260 HOH A 309 SITE 1 AC2 11 ALA A 7 ALA A 11 ALA A 19 GLY A 20 SITE 2 AC2 11 TYR A 83 TRP A 93 HOH A 209 HOH A 236 SITE 3 AC2 11 HOH A 264 HOH A 266 HOH A 279 CRYST1 31.781 27.637 44.099 90.00 101.16 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 0.031465 0.000000 0.006210 0.00000 SCALE2 0.000000 0.036183 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023114 0.00000