HEADER TRANSPORT PROTEIN 22-APR-09 3A1W TITLE CRYSTAL STRUCTUE OF THE G DOMAIN OF T. MARITIMA FEOB IRON IRANSPORTER COMPND MOL_ID: 1; COMPND 2 MOLECULE: IRON(II) TRANSPORT PROTEIN B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 17-269; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: TM0051; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: C41(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS FEOB, IRON TRANSPORTER, SMALL GTPASE, GDI, G PROTEIN, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.HATTORI,R.ISHITANI,O.NUREKI REVDAT 3 01-NOV-23 3A1W 1 REMARK SEQADV REVDAT 2 03-NOV-09 3A1W 1 JRNL REVDAT 1 22-SEP-09 3A1W 0 JRNL AUTH M.HATTORI,Y.JIN,H.NISHIMASU,Y.TANAKA,M.MOCHIZUKI,T.UCHIUMI, JRNL AUTH 2 R.ISHITANI,K.ITO,O.NUREKI JRNL TITL STRUCTURAL BASIS OF NOVEL INTERACTIONS BETWEEN THE JRNL TITL 2 SMALL-GTPASE AND GDI-LIKE DOMAINS IN PROKARYOTIC FEOB IRON JRNL TITL 3 TRANSPORTER JRNL REF STRUCTURE V. 17 1345 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 19733088 JRNL DOI 10.1016/J.STR.2009.08.007 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 19031 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 952 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 41.7559 - 3.6335 0.99 2788 147 0.1820 0.2112 REMARK 3 2 3.6335 - 2.8842 1.00 2634 139 0.1664 0.1992 REMARK 3 3 2.8842 - 2.5197 0.99 2611 138 0.1826 0.2152 REMARK 3 4 2.5197 - 2.2893 0.99 2565 134 0.1804 0.2202 REMARK 3 5 2.2893 - 2.1253 0.98 2542 134 0.1972 0.2456 REMARK 3 6 2.1253 - 2.0000 0.97 2510 133 0.2240 0.2488 REMARK 3 7 2.0000 - 1.8998 0.95 2429 127 0.2808 0.3114 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 : 0.39 REMARK 3 B_SOL : 77.78 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.690 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 1269 REMARK 3 ANGLE : 1.036 1730 REMARK 3 CHIRALITY : 0.068 208 REMARK 3 PLANARITY : 0.003 218 REMARK 3 DIHEDRAL : 17.501 451 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A 15-177 REMARK 3 ORIGIN FOR THE GROUP (A): 2.1148 -21.5756 -17.9074 REMARK 3 T TENSOR REMARK 3 T11: 0.1317 T22: 0.3077 REMARK 3 T33: 0.2238 T12: -0.0043 REMARK 3 T13: 0.0353 T23: -0.0168 REMARK 3 L TENSOR REMARK 3 L11: 3.0398 L22: 1.3520 REMARK 3 L33: 3.6990 L12: -0.4972 REMARK 3 L13: -1.8213 L23: 0.3652 REMARK 3 S TENSOR REMARK 3 S11: -0.2394 S12: -0.0749 S13: -0.1812 REMARK 3 S21: 0.0141 S22: -0.0516 S23: 0.1051 REMARK 3 S31: 0.2113 S32: -0.2075 S33: 0.2427 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 3A1W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000028707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JAN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21851 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3A1S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.1-1.3M AMMONIUM SULFATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 58.44100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.58750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.58750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.22050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.58750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.58750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 87.66150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.58750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.58750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.22050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.58750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.58750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 87.66150 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.44100 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 GLY A 12 REMARK 465 PRO A 13 REMARK 465 LEU A 14 REMARK 465 THR A 137 REMARK 465 GLY A 138 REMARK 465 MET A 139 REMARK 465 LYS A 140 REMARK 465 LYS A 178 REMARK 465 ASN A 179 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 LYS A 84 CG CD CE NZ REMARK 470 ASP A 132 CG OD1 OD2 REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 LYS A 136 CG CD CE NZ REMARK 470 TYR A 144 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 145 CG CD OE1 OE2 REMARK 470 LYS A 148 CG CD CE 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 OE1 GLU A 167 O HOH A 240 6544 1.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AIS RELATED DB: PDB REMARK 900 RELATED ID: 3AIT RELATED DB: PDB REMARK 900 RELATED ID: 3AIU RELATED DB: PDB REMARK 900 RELATED ID: 3AIV RELATED DB: PDB DBREF 3A1W A 17 179 UNP Q9WXQ8 Q9WXQ8_THEMA 17 179 SEQADV 3A1W GLY A 12 UNP Q9WXQ8 EXPRESSION TAG SEQADV 3A1W PRO A 13 UNP Q9WXQ8 EXPRESSION TAG SEQADV 3A1W LEU A 14 UNP Q9WXQ8 EXPRESSION TAG SEQADV 3A1W HIS A 15 UNP Q9WXQ8 EXPRESSION TAG SEQADV 3A1W MET A 16 UNP Q9WXQ8 EXPRESSION TAG SEQRES 1 A 168 GLY PRO LEU HIS MET VAL LYS VAL ALA LEU ALA GLY CYS SEQRES 2 A 168 PRO ASN VAL GLY LYS THR SER LEU PHE ASN ALA LEU THR SEQRES 3 A 168 GLY THR LYS GLN TYR VAL ALA ASN TRP PRO GLY VAL THR SEQRES 4 A 168 VAL GLU LYS LYS GLU GLY VAL PHE THR TYR LYS GLY TYR SEQRES 5 A 168 THR ILE ASN LEU ILE ASP LEU PRO GLY THR TYR SER LEU SEQRES 6 A 168 GLY TYR SER SER ILE ASP GLU LYS ILE ALA ARG ASP TYR SEQRES 7 A 168 LEU LEU LYS GLY ASP ALA ASP LEU VAL ILE LEU VAL ALA SEQRES 8 A 168 ASP SER VAL ASN PRO GLU GLN SER LEU TYR LEU LEU LEU SEQRES 9 A 168 GLU ILE LEU GLU MET GLU LYS LYS VAL ILE LEU ALA MET SEQRES 10 A 168 THR ALA ILE ASP GLU ALA LYS LYS THR GLY MET LYS ILE SEQRES 11 A 168 ASP ARG TYR GLU LEU GLN LYS HIS LEU GLY ILE PRO VAL SEQRES 12 A 168 VAL PHE THR SER SER VAL THR GLY GLU GLY LEU GLU GLU SEQRES 13 A 168 LEU LYS GLU LYS ILE VAL GLU TYR ALA GLN LYS ASN HET SO4 A 1 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *104(H2 O) HELIX 1 1 GLY A 28 GLY A 38 1 11 HELIX 2 2 SER A 80 LYS A 92 1 13 HELIX 3 3 PRO A 107 GLU A 121 1 15 HELIX 4 4 ALA A 130 LYS A 136 1 7 HELIX 5 5 ASP A 142 GLY A 151 1 10 HELIX 6 6 GLY A 164 GLN A 177 1 14 SHEET 1 A 7 GLN A 41 ASN A 45 0 SHEET 2 A 7 GLU A 52 TYR A 60 -1 O LYS A 53 N ALA A 44 SHEET 3 A 7 TYR A 63 ASP A 69 -1 O ILE A 65 N PHE A 58 SHEET 4 A 7 MET A 16 GLY A 23 1 N VAL A 17 O ASN A 66 SHEET 5 A 7 LEU A 97 ASP A 103 1 O VAL A 101 N ALA A 22 SHEET 6 A 7 VAL A 124 THR A 129 1 O ILE A 125 N LEU A 100 SHEET 7 A 7 VAL A 154 PHE A 156 1 O VAL A 155 N LEU A 126 SITE 1 AC1 8 HOH A 3 ASN A 26 VAL A 27 GLY A 28 SITE 2 AC1 8 LYS A 29 THR A 30 HOH A 195 HOH A 202 CRYST1 63.175 63.175 116.882 90.00 90.00 90.00 P 41 21 2 8 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 0.015829 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008556 0.00000