HEADER ELECTRON TRANSPORT 15-JUN-18 6A3K TITLE CRYSTAL STRUCTURE OF CYTOCHROME C' FROM SHEWANELLA BENTHICA DB6705 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA BENTHICA DB6705; SOURCE 3 ORGANISM_TAXID: 126830; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 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 6A3K 1 COMPND REMARK HET HETNAM REVDAT 2 2 1 HETSYN FORMUL LINK ATOM REVDAT 1 12-JUN-19 6A3K 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. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 15035 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1494 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 21.2644 - 3.7965 0.99 1265 152 0.1394 0.1375 REMARK 3 2 3.7965 - 3.0161 1.00 1253 144 0.1444 0.1824 REMARK 3 3 3.0161 - 2.6357 1.00 1253 142 0.1694 0.2080 REMARK 3 4 2.6357 - 2.3950 1.00 1242 146 0.1724 0.2121 REMARK 3 5 2.3950 - 2.2236 1.00 1260 124 0.1736 0.2322 REMARK 3 6 2.2236 - 2.0926 1.00 1257 129 0.1669 0.2199 REMARK 3 7 2.0926 - 1.9879 1.00 1241 137 0.2001 0.2333 REMARK 3 8 1.9879 - 1.9014 1.00 1249 125 0.1748 0.2265 REMARK 3 9 1.9014 - 1.8282 1.00 1250 125 0.1917 0.2277 REMARK 3 10 1.8282 - 1.7652 0.99 1231 148 0.2224 0.2996 REMARK 3 11 1.7652 - 1.7100 0.85 1040 122 0.2983 0.3424 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.03 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 : 0.006 1127 REMARK 3 ANGLE : 0.884 1522 REMARK 3 CHIRALITY : 0.038 153 REMARK 3 PLANARITY : 0.005 191 REMARK 3 DIHEDRAL : 17.208 434 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6A3K 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_1300007837. 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 : 10.5 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 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 : 15047 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 37.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.14 REMARK 200 R MERGE FOR SHELL (I) : 0.21400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 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 (%): 50.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CAPS (PH 10.5), 30% (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: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 36.33600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.23500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.33600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.23500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 452 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 470 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 483 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 526 LIES ON A SPECIAL POSITION. 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 526 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A 527 DISTANCE = 5.91 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 95.9 REMARK 620 3 HEC A 201 NB 96.5 90.7 REMARK 620 4 HEC A 201 NC 95.3 168.8 88.5 REMARK 620 5 HEC A 201 ND 96.0 87.9 167.5 90.4 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 residue 1PE A 202 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE IS REGISTERED WITH ACCESSION ID LC406697 IN DDBJ. DBREF 6A3K A 1 129 PDB 6A3K 6A3K 1 129 SEQRES 1 A 129 SER 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 ALA MET ARG ALA GLN ASN VAL ALA ALA LEU SEQRES 5 A 129 SER LYS LEU PRO LEU GLU GLY PHE ILE PRO GLY SER ASP SEQRES 6 A 129 GLN GLY GLU THR GLU ALA LEU ALA LYS ILE TRP THR GLU SEQRES 7 A 129 LYS SER ASP PHE ASP ALA LYS MET LYS THR 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 GLN VAL ALA LYS SEQRES 10 A 129 SER CYS LYS GLY CYS HIS ASP VAL TYR LYS LYS ASP HET HEC A 201 43 HET 1PE A 202 16 HETNAM HEC HEME C HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 2 HEC C34 H34 FE N4 O4 FORMUL 3 1PE C10 H22 O6 FORMUL 4 HOH *227(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 LEU A 72 TRP A 76 5 5 HELIX 5 AA5 GLU A 78 SER A 100 1 23 HELIX 6 AA6 ASP A 104 LYS A 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 1.78 LINK NE2 HIS A 123 FE HEC A 201 1555 1555 2.14 SITE 1 AC1 18 ARG A 13 GLN A 14 PHE A 17 MET A 20 SITE 2 AC1 18 ALA A 21 PHE A 60 THR A 69 GLU A 70 SITE 3 AC1 18 PHE A 82 SER A 118 CYS A 119 CYS A 122 SITE 4 AC1 18 HIS A 123 LYS A 127 HOH A 321 HOH A 332 SITE 5 AC1 18 HOH A 351 HOH A 359 SITE 1 AC2 7 ASN A 2 MET A 44 LEU A 57 GLU A 58 SITE 2 AC2 7 PHE A 60 LYS A 79 HOH A 383 CRYST1 72.672 52.470 50.929 90.00 132.85 90.00 C 1 2 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 0.013760 0.000000 0.012765 0.00000 SCALE2 0.000000 0.019059 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026783 0.00000