HEADER METAL BINDING PROTEIN 07-AUG-11 3TBN TITLE CRYSTAL STRUCTURE OF A MINER2 HOMOLOG: A TYPE 6 CDGSH IRON-SULFUR TITLE 2 PROTEIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TYPE 6 CDGSH IRON-SULFUR PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MAGNETOSPIRILLUM MAGNETICUM; SOURCE 3 ORGANISM_TAXID: 342108; SOURCE 4 STRAIN: AMB-1; SOURCE 5 GENE: AMB400, AMB4007; 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 CDGSH, IRON-SULFUR, MINER2, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LIN,L.ZHANG,K.YE REVDAT 3 20-MAR-24 3TBN 1 REMARK SEQADV LINK REVDAT 2 12-OCT-11 3TBN 1 JRNL REVDAT 1 05-OCT-11 3TBN 0 JRNL AUTH J.LIN,L.ZHANG,S.LAI,K.YE JRNL TITL STRUCTURE AND MOLECULAR EVOLUTION OF CDGSH IRON-SULFUR JRNL TITL 2 DOMAINS. JRNL REF PLOS ONE V. 6 24790 2011 JRNL REFN ESSN 1932-6203 JRNL PMID 21949752 JRNL DOI 10.1371/JOURNAL.PONE.0024790 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 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) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 37842 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.112 REMARK 3 R VALUE (WORKING SET) : 0.111 REMARK 3 FREE R VALUE : 0.125 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1881 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 14.0580 - 2.6982 0.83 2492 129 0.1494 0.1674 REMARK 3 2 2.6982 - 2.1441 0.95 2808 147 0.1097 0.1136 REMARK 3 3 2.1441 - 1.8738 0.96 2809 140 0.0950 0.0994 REMARK 3 4 1.8738 - 1.7028 0.96 2832 135 0.0803 0.1013 REMARK 3 5 1.7028 - 1.5809 0.97 2820 136 0.0798 0.1035 REMARK 3 6 1.5809 - 1.4878 0.97 2843 135 0.0868 0.1000 REMARK 3 7 1.4878 - 1.4134 0.97 2799 173 0.0911 0.1076 REMARK 3 8 1.4134 - 1.3519 0.97 2805 160 0.0946 0.1195 REMARK 3 9 1.3519 - 1.2999 0.97 2810 156 0.1039 0.1274 REMARK 3 10 1.2999 - 1.2551 0.96 2807 132 0.1088 0.1418 REMARK 3 11 1.2551 - 1.2158 0.96 2800 150 0.1279 0.1265 REMARK 3 12 1.2158 - 1.1811 0.96 2785 152 0.1462 0.1473 REMARK 3 13 1.1811 - 1.1500 0.87 2551 136 0.1914 0.1688 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 77.98 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 8.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.26250 REMARK 3 B22 (A**2) : 0.26250 REMARK 3 B33 (A**2) : -0.52500 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 : 0.005 677 REMARK 3 ANGLE : 1.707 919 REMARK 3 CHIRALITY : 0.059 94 REMARK 3 PLANARITY : 0.006 118 REMARK 3 DIHEDRAL : 20.924 409 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3TBN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067281. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39768 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.49400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.0M SODIUM FORMATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.71200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.35600 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.53400 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 8.17800 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.89000 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 31 NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HE2 HIS A -3 H TYR A 59 4655 1.31 REMARK 500 REMARK 500 REMARK: NULL 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 FES A 80 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 25 SG REMARK 620 2 FES A 80 S1 112.6 REMARK 620 3 FES A 80 S2 117.4 105.6 REMARK 620 4 CYS A 27 SG 100.3 108.3 112.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 80 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 36 SG REMARK 620 2 FES A 80 S1 110.7 REMARK 620 3 FES A 80 S2 123.2 104.9 REMARK 620 4 HIS A 40 ND1 96.1 115.4 106.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 81 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 61 SG REMARK 620 2 FES A 81 S1 115.2 REMARK 620 3 FES A 81 S2 116.0 104.8 REMARK 620 4 CYS A 63 SG 99.8 113.5 107.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 81 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 72 SG REMARK 620 2 FES A 81 S1 121.7 REMARK 620 3 FES A 81 S2 113.1 104.4 REMARK 620 4 HIS A 76 ND1 96.4 104.3 117.2 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 FES A 80 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES A 81 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TBM RELATED DB: PDB REMARK 900 RELATED ID: 3TBO RELATED DB: PDB DBREF 3TBN A 2 79 UNP Q2W014 Q2W014_MAGSA 2 79 SEQADV 3TBN GLY A -7 UNP Q2W014 EXPRESSION TAG SEQADV 3TBN SER A -6 UNP Q2W014 EXPRESSION TAG SEQADV 3TBN SER A -5 UNP Q2W014 EXPRESSION TAG SEQADV 3TBN HIS A -4 UNP Q2W014 EXPRESSION TAG SEQADV 3TBN HIS A -3 UNP Q2W014 EXPRESSION TAG SEQADV 3TBN HIS A -2 UNP Q2W014 EXPRESSION TAG SEQADV 3TBN HIS A -1 UNP Q2W014 EXPRESSION TAG SEQADV 3TBN HIS A 0 UNP Q2W014 EXPRESSION TAG SEQADV 3TBN HIS A 1 UNP Q2W014 EXPRESSION TAG SEQRES 1 A 87 GLY SER SER HIS HIS HIS HIS HIS HIS THR ASP PRO VAL SEQRES 2 A 87 ILE ALA GLN LYS ALA PRO TYR PRO VAL THR VAL GLU ALA SEQRES 3 A 87 GLY LYS THR TYR HIS TRP CYS ALA CYS GLY ARG SER LYS SEQRES 4 A 87 ALA GLN PRO PHE CYS ASP GLY SER HIS LYS GLY THR GLY SEQRES 5 A 87 LEU ALA PRO VAL ALA TYR THR PRO ASP LYS ALA GLY THR SEQRES 6 A 87 ALA TYR PHE CYS GLY CYS LYS ALA SER LYS ALA PRO PRO SEQRES 7 A 87 LEU CYS ASP GLY THR HIS LYS THR LEU HET FES A 80 4 HET FES A 81 4 HETNAM FES FE2/S2 (INORGANIC) CLUSTER FORMUL 2 FES 2(FE2 S2) FORMUL 4 HOH *152(H2 O) HELIX 1 1 GLY A 74 THR A 78 5 5 SHEET 1 A 2 TYR A 12 VAL A 16 0 SHEET 2 A 2 GLY A 56 PHE A 60 -1 O GLY A 56 N VAL A 16 SHEET 1 B 2 TYR A 22 TRP A 24 0 SHEET 2 B 2 VAL A 48 TYR A 50 -1 O TYR A 50 N TYR A 22 LINK SG CYS A 25 FE2 FES A 80 1555 1555 2.37 LINK SG CYS A 27 FE2 FES A 80 1555 1555 2.35 LINK SG CYS A 36 FE1 FES A 80 1555 1555 2.34 LINK ND1 HIS A 40 FE1 FES A 80 1555 1555 2.14 LINK SG CYS A 61 FE2 FES A 81 1555 1555 2.36 LINK SG CYS A 63 FE2 FES A 81 1555 1555 2.37 LINK SG CYS A 72 FE1 FES A 81 1555 1555 2.33 LINK ND1 HIS A 76 FE1 FES A 81 1555 1555 2.15 CISPEP 1 GLN A 33 PRO A 34 0 6.98 CISPEP 2 PRO A 69 PRO A 70 0 8.56 SITE 1 AC1 9 CYS A 25 ALA A 26 CYS A 27 CYS A 36 SITE 2 AC1 9 ASP A 37 GLY A 38 SER A 39 HIS A 40 SITE 3 AC1 9 PRO A 47 SITE 1 AC2 10 ALA A 10 PRO A 11 CYS A 61 GLY A 62 SITE 2 AC2 10 CYS A 63 CYS A 72 ASP A 73 GLY A 74 SITE 3 AC2 10 THR A 75 HIS A 76 CRYST1 63.498 63.498 49.068 90.00 90.00 120.00 P 65 6 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 0.015749 0.009092 0.000000 0.00000 SCALE2 0.000000 0.018185 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020380 0.00000