HEADER ELECTRON TRANSPORT 15-JUN-18 6A3L TITLE CRYSTAL STRUCTURE OF CYTOCHROME C' FROM SHEWANELLA VIOLACEA DSS12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA VIOLACEA (STRAIN JCM 10179 / CIP SOURCE 3 106290 / LMG 19151 / DSS12); SOURCE 4 ORGANISM_TAXID: 637905; SOURCE 5 STRAIN: JCM 10179 / CIP 106290 / LMG 19151 / DSS12; SOURCE 6 GENE: SVI_0970; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYTOCHROME C', SHEWANELLA, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.SUKA,H.OKI,Y.KATO,K.KAWAHARA,T.OHKUBO,T.MARUNO,Y.KOBAYASHI,S.FUJII, AUTHOR 2 S.WAKAI,Y.SAMBONGI REVDAT 2 02-OCT-19 6A3L 1 COMPND REMARK HET HETNAM REVDAT 2 2 1 HETSYN FORMUL LINK ATOM REVDAT 1 12-JUN-19 6A3L 0 JRNL AUTH A.SUKA,H.OKI,Y.KATO,K.KAWAHARA,T.OHKUBO,T.MARUNO, JRNL AUTH 2 Y.KOBAYASHI,S.FUJII,S.WAKAI,L.LISDIANA,Y.SAMBONGI JRNL TITL STABILITY OF CYTOCHROMES C' FROM PSYCHROPHILIC AND JRNL TITL 2 PIEZOPHILIC SHEWANELLA SPECIES: IMPLICATIONS FOR COMPLEX JRNL TITL 3 MULTIPLE ADAPTATION TO LOW TEMPERATURE AND HIGH HYDROSTATIC JRNL TITL 4 PRESSURE. JRNL REF EXTREMOPHILES V. 23 239 2019 JRNL REFN ESSN 1433-4909 JRNL PMID 30689055 JRNL DOI 10.1007/S00792-019-01077-9 REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 14188 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1423 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 22.5729 - 4.5989 0.99 1311 145 0.1495 0.1972 REMARK 3 2 4.5989 - 3.6553 1.00 1300 150 0.1610 0.2050 REMARK 3 3 3.6553 - 3.1947 0.99 1272 143 0.2023 0.2703 REMARK 3 4 3.1947 - 2.9033 1.00 1308 144 0.2653 0.3374 REMARK 3 5 2.9033 - 2.6956 0.99 1257 149 0.2808 0.3771 REMARK 3 6 2.6956 - 2.5369 0.99 1284 137 0.2849 0.3509 REMARK 3 7 2.5369 - 2.4100 0.99 1276 144 0.2875 0.3670 REMARK 3 8 2.4100 - 2.3052 0.98 1267 139 0.3022 0.4077 REMARK 3 9 2.3052 - 2.2165 0.97 1249 139 0.3383 0.3614 REMARK 3 10 2.2165 - 2.1401 0.97 1241 133 0.3590 0.3462 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.20 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 2118 REMARK 3 ANGLE : 1.078 2854 REMARK 3 CHIRALITY : 0.056 290 REMARK 3 PLANARITY : 0.007 360 REMARK 3 DIHEDRAL : 22.478 764 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 1146 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6A3L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1300007835. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.4 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.9.9.8 W9DSSI REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14369 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 REMARK 200 RESOLUTION RANGE LOW (A) : 37.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.250 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.22 REMARK 200 R MERGE FOR SHELL (I) : 0.45100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CAPS (PH 9.4), 26 % (V/V) PEG REMARK 280 400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 34.85350 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 A 335 DISTANCE = 6.25 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 123 NE2 REMARK 620 2 HEC A 201 NA 98.6 REMARK 620 3 HEC A 201 NB 91.2 90.8 REMARK 620 4 HEC A 201 NC 93.2 168.1 87.8 REMARK 620 5 HEC A 201 ND 101.1 87.5 167.7 91.4 REMARK 620 N 1 2 3 4 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 123 NE2 REMARK 620 2 HEC B 201 NA 95.2 REMARK 620 3 HEC B 201 NB 90.7 92.5 REMARK 620 4 HEC B 201 NC 93.2 171.6 87.2 REMARK 620 5 HEC B 201 ND 97.0 87.3 172.2 91.8 REMARK 620 N 1 2 3 4 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 Di-peptide HEM B 201 and CYS B REMARK 800 122 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide HEM B 201 and CYS B REMARK 800 119 DBREF 6A3L A 1 129 UNP D4ZGZ2 D4ZGZ2_SHEVD 19 147 DBREF 6A3L B 1 129 UNP D4ZGZ2 D4ZGZ2_SHEVD 19 147 SEQRES 1 A 129 GLY ASN PHE LYS GLU ALA ASP ASP ALA ILE HIS TYR ARG SEQRES 2 A 129 GLN SER ALA PHE SER LEU MET ALA HIS ASN PHE GLY ASP SEQRES 3 A 129 MET GLY ALA MET LEU LYS GLY LYS LYS PRO PHE ASP SER SEQRES 4 A 129 GLU ILE PHE THR MET ARG ALA GLU ASN VAL ALA ALA LEU SEQRES 5 A 129 SER LYS LEU PRO LEU GLU GLY PHE ILE GLN GLY SER ASP SEQRES 6 A 129 LEU GLY ASP THR GLU ALA LEU ALA LYS ILE TRP THR ASP SEQRES 7 A 129 LYS SER ASP PHE ASP ALA LYS MET VAL SER LEU GLN ASP SEQRES 8 A 129 ASN ALA ALA ALA LEU LEU LEU ALA SER ALA SER ASP ASP SEQRES 9 A 129 LYS LYS LEU LEU LYS GLN SER PHE MET LYS VAL ALA LYS SEQRES 10 A 129 SER CYS LYS GLY CYS HIS ASP VAL TYR LYS LYS ASP SEQRES 1 B 129 GLY ASN PHE LYS GLU ALA ASP ASP ALA ILE HIS TYR ARG SEQRES 2 B 129 GLN SER ALA PHE SER LEU MET ALA HIS ASN PHE GLY ASP SEQRES 3 B 129 MET GLY ALA MET LEU LYS GLY LYS LYS PRO PHE ASP SER SEQRES 4 B 129 GLU ILE PHE THR MET ARG ALA GLU ASN VAL ALA ALA LEU SEQRES 5 B 129 SER LYS LEU PRO LEU GLU GLY PHE ILE GLN GLY SER ASP SEQRES 6 B 129 LEU GLY ASP THR GLU ALA LEU ALA LYS ILE TRP THR ASP SEQRES 7 B 129 LYS SER ASP PHE ASP ALA LYS MET VAL SER LEU GLN ASP SEQRES 8 B 129 ASN ALA ALA ALA LEU LEU LEU ALA SER ALA SER ASP ASP SEQRES 9 B 129 LYS LYS LEU LEU LYS GLN SER PHE MET LYS VAL ALA LYS SEQRES 10 B 129 SER CYS LYS GLY CYS HIS ASP VAL TYR LYS LYS ASP HET HEC A 201 43 HET HEC B 201 43 HETNAM HEC HEME C FORMUL 3 HEC 2(C34 H34 FE N4 O4) FORMUL 5 HOH *70(H2 O) HELIX 1 AA1 GLU A 5 LYS A 32 1 28 HELIX 2 AA2 ASP A 38 LYS A 54 1 17 HELIX 3 AA3 LEU A 55 PHE A 60 5 6 HELIX 4 AA4 ALA A 73 ASP A 78 1 6 HELIX 5 AA5 ASP A 78 SER A 100 1 23 HELIX 6 AA6 ASP A 104 LYS A 127 1 24 HELIX 7 AA7 GLU B 5 LYS B 32 1 28 HELIX 8 AA8 ASP B 38 LYS B 54 1 17 HELIX 9 AA9 LEU B 55 PHE B 60 5 6 HELIX 10 AB1 ALA B 73 ASP B 78 1 6 HELIX 11 AB2 ASP B 78 SER B 100 1 23 HELIX 12 AB3 ASP B 104 LYS B 127 1 24 LINK SG CYS A 119 CAB HEC A 201 1555 1555 1.77 LINK SG CYS A 122 CAC HEC A 201 1555 1555 1.77 LINK NE2 HIS A 123 FE HEC A 201 1555 1555 2.14 LINK SG CYS B 119 CAB HEC B 201 1555 1555 1.77 LINK SG CYS B 122 CAC HEC B 201 1555 1555 1.77 LINK NE2 HIS B 123 FE HEC B 201 1555 1555 2.29 SITE 1 AC1 15 ARG A 13 GLN A 14 PHE A 17 MET A 20 SITE 2 AC1 15 ALA A 21 PHE A 60 THR A 69 GLU A 70 SITE 3 AC1 15 PHE A 82 MET A 86 LEU A 89 CYS A 119 SITE 4 AC1 15 CYS A 122 HIS A 123 HOH A 305 SITE 1 AC2 19 ARG B 13 GLN B 14 PHE B 17 MET B 20 SITE 2 AC2 19 ALA B 21 PHE B 60 THR B 69 GLU B 70 SITE 3 AC2 19 PHE B 82 LEU B 89 SER B 118 CYS B 119 SITE 4 AC2 19 LYS B 120 GLY B 121 HIS B 123 ASP B 124 SITE 5 AC2 19 VAL B 125 TYR B 126 HOH B 303 SITE 1 AC3 19 ARG B 13 GLN B 14 PHE B 17 MET B 20 SITE 2 AC3 19 ALA B 21 PHE B 60 THR B 69 GLU B 70 SITE 3 AC3 19 PHE B 82 LEU B 89 VAL B 115 ALA B 116 SITE 4 AC3 19 LYS B 117 SER B 118 LYS B 120 GLY B 121 SITE 5 AC3 19 CYS B 122 HIS B 123 HOH B 303 CRYST1 44.751 69.707 45.598 90.00 112.19 90.00 P 1 21 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 0.022346 0.000000 0.009115 0.00000 SCALE2 0.000000 0.014346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023685 0.00000