HEADER ELECTRON TRANSPORT 19-FEB-14 4OV1 TITLE THE CRYSTAL STRUCTURE OF A NOVEL ELECTRON TRANSFER FERREDOXIN FROM R. TITLE 2 PALUSTRIS HAA2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE FERREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOPSEUDOMONAS PALUSTRIS; SOURCE 3 ORGANISM_TAXID: 316058; SOURCE 4 STRAIN: HAA2; SOURCE 5 GENE: RPB_3630; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS 3FE-4S SINGLE CLUSTER DOMAIN, PUTATIVE FERREDOXIN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR W.H.ZHOUW,T.ZHANG,A.L.ZHANG,S.G.BELL,L.-L.WONG REVDAT 3 08-NOV-23 4OV1 1 REMARK LINK REVDAT 2 25-DEC-19 4OV1 1 JRNL REVDAT 1 21-MAY-14 4OV1 0 JRNL AUTH T.ZHANG,A.L.ZHANG,S.G.BELL,L.-L.WONG,W.H.ZHOU JRNL TITL THE STRUCTURE OF A NOVEL ELECTRON-TRANSFER FERREDOXIN FROM JRNL TITL 2 RHODOPSEUDOMONAS PALUSTRIS HAA2 WHICH CONTAINS A HISTIDINE JRNL TITL 3 RESIDUE IN ITS IRON-SULFUR CLUSTER-BINDING MOTIF. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 1453 2014 JRNL REFN ESSN 1399-0047 JRNL PMID 24816113 JRNL DOI 10.1107/S139900471400474X REMARK 2 REMARK 2 RESOLUTION. 2.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.2_432) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 2671 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 266 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 23.1121 - 2.9049 0.99 1287 144 0.2080 0.2061 REMARK 3 2 2.9049 - 2.3064 0.91 1118 122 0.2571 0.3485 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 39.37 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -11.33580 REMARK 3 B22 (A**2) : 27.38290 REMARK 3 B33 (A**2) : -16.04710 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.014 521 REMARK 3 ANGLE : 1.503 704 REMARK 3 CHIRALITY : 0.063 77 REMARK 3 PLANARITY : 0.006 94 REMARK 3 DIHEDRAL : 12.461 191 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 4:44) REMARK 3 ORIGIN FOR THE GROUP (A): -0.5823 7.4107 -7.4526 REMARK 3 T TENSOR REMARK 3 T11: 0.1719 T22: 0.2538 REMARK 3 T33: 0.2075 T12: 0.0002 REMARK 3 T13: 0.0310 T23: 0.0126 REMARK 3 L TENSOR REMARK 3 L11: 1.1895 L22: 0.4947 REMARK 3 L33: 2.9121 L12: 0.3088 REMARK 3 L13: 1.4784 L23: -0.1048 REMARK 3 S TENSOR REMARK 3 S11: 0.0442 S12: -0.2777 S13: -0.0796 REMARK 3 S21: 0.0171 S22: -0.0216 S23: 0.0063 REMARK 3 S31: -0.0397 S32: -0.1765 S33: -0.0462 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 45:69) REMARK 3 ORIGIN FOR THE GROUP (A): 0.0448 6.7685 -17.3154 REMARK 3 T TENSOR REMARK 3 T11: 0.2022 T22: 0.2308 REMARK 3 T33: 0.1731 T12: -0.0228 REMARK 3 T13: 0.0083 T23: -0.0208 REMARK 3 L TENSOR REMARK 3 L11: 1.3629 L22: 4.8116 REMARK 3 L33: 1.3556 L12: -2.2307 REMARK 3 L13: 0.4190 L23: -1.8204 REMARK 3 S TENSOR REMARK 3 S11: 0.1449 S12: 0.2049 S13: 0.0060 REMARK 3 S21: -0.3304 S22: -0.1427 S23: -0.0930 REMARK 3 S31: 0.0095 S32: -0.0415 S33: -0.0270 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 4OV1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000084983. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2832 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.12600 REMARK 200 R SYM FOR SHELL (I) : 0.12600 REMARK 200 FOR SHELL : 12.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 2Z8Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3M POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, 0.1M TRIS PH 8.5, 2.4M AMMONIUM SULFATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 11.68100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.59600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.40500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.59600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.68100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 13.40500 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 GLU A 3 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 4 SD CE 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 F3S A 101 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 14 SG REMARK 620 2 F3S A 101 S1 111.7 REMARK 620 3 F3S A 101 S2 112.4 119.3 REMARK 620 4 F3S A 101 S3 110.3 101.2 100.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S A 101 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 20 SG REMARK 620 2 F3S A 101 S1 103.7 REMARK 620 3 F3S A 101 S3 122.5 101.6 REMARK 620 4 F3S A 101 S4 111.7 114.1 103.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F3S A 101 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 59 SG REMARK 620 2 F3S A 101 S2 105.3 REMARK 620 3 F3S A 101 S3 112.4 99.9 REMARK 620 4 F3S A 101 S4 117.7 117.6 102.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F3S A 101 DBREF 4OV1 A 1 69 UNP Q2ITY5 Q2ITY5_RHOP2 1 69 SEQRES 1 A 69 MET SER GLU MET LEU THR ILE HIS VAL ASP GLN ASP LYS SEQRES 2 A 69 CYS GLN GLY HIS ALA ARG CYS LYS ALA LEU ALA PRO GLU SEQRES 3 A 69 LEU PHE ASP LEU ASP ASP TYR GLY ASN ALA HIS GLU LYS SEQRES 4 A 69 GLY ASP GLY VAL VAL PRO ALA ASP LEU ILE ASP LYS ALA SEQRES 5 A 69 TRP LEU ALA LYS SER ASN CYS PRO GLU ASN ALA ILE ASP SEQRES 6 A 69 ILE THR GLU ASP HET F3S A 101 7 HETNAM F3S FE3-S4 CLUSTER FORMUL 2 F3S FE3 S4 FORMUL 3 HOH *13(H2 O) HELIX 1 1 ALA A 18 ALA A 24 1 7 HELIX 2 2 PRO A 45 ASP A 47 5 3 HELIX 3 3 LEU A 48 CYS A 59 1 12 SHEET 1 A 2 LEU A 5 VAL A 9 0 SHEET 2 A 2 ILE A 64 GLU A 68 -1 O ASP A 65 N HIS A 8 SHEET 1 B 2 PHE A 28 LEU A 30 0 SHEET 2 B 2 ALA A 36 GLU A 38 -1 O HIS A 37 N ASP A 29 LINK SG CYS A 14 FE1 F3S A 101 1555 1555 2.39 LINK SG CYS A 20 FE3 F3S A 101 1555 1555 2.30 LINK SG CYS A 59 FE4 F3S A 101 1555 1555 2.25 SITE 1 AC1 8 CYS A 14 GLN A 15 GLY A 16 HIS A 17 SITE 2 AC1 8 ALA A 18 ARG A 19 CYS A 20 CYS A 59 CRYST1 23.362 26.810 91.192 90.00 90.00 90.00 P 21 21 21 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 0.042805 0.000000 0.000000 0.00000 SCALE2 0.000000 0.037300 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010966 0.00000