HEADER METAL TRANSPORT 24-JUN-21 7R7B TITLE 1.50 ANGSTROEM CRYSTAL STRUCTURE OF FEOA FROM BACTEROIDES FRAGILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERROUS IRON TRANSPORT PROTEIN B; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES FRAGILIS; SOURCE 3 ORGANISM_TAXID: 817; SOURCE 4 GENE: FEOB, BUN20_04310, DW228_07360, DXB57_02360, EC80_0207810, SOURCE 5 EE52_0204010, EE52_020515, FOC69_09580, IA74_010110, IB64_011160; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FEO, SH3, MEMBRANE TRANSPORTER, METAL TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.E.SESTOK,A.T.SMITH REVDAT 2 18-OCT-23 7R7B 1 REMARK REVDAT 1 27-APR-22 7R7B 0 JRNL AUTH A.E.SESTOK,J.B.BROWN,J.O.OBI,S.M.O'SULLIVAN,E.D.GARCIN, JRNL AUTH 2 D.J.DEREDGE,A.T.SMITH JRNL TITL A FUSION OF THE BACTEROIDES FRAGILIS FERROUS IRON IMPORT JRNL TITL 2 PROTEINS REVEALS A ROLE FOR FEOA IN STABILIZING GTP-BOUND JRNL TITL 3 FEOB. JRNL REF J.BIOL.CHEM. V. 298 01808 2022 JRNL REFN ESSN 1083-351X JRNL PMID 35271852 JRNL DOI 10.1016/J.JBC.2022.101808 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 23050 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 1100 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 36.0300 - 3.0000 1.00 2873 118 0.1648 0.1974 REMARK 3 2 3.0000 - 2.3800 1.00 2740 163 0.1972 0.2356 REMARK 3 3 2.3800 - 2.0800 1.00 2771 129 0.1920 0.2218 REMARK 3 4 2.0800 - 1.8900 1.00 2717 154 0.1972 0.2397 REMARK 3 5 1.8900 - 1.7500 1.00 2737 135 0.1997 0.2435 REMARK 3 6 1.7500 - 1.6500 1.00 2725 123 0.2261 0.2212 REMARK 3 7 1.6500 - 1.5700 1.00 2694 130 0.2528 0.3196 REMARK 3 8 1.5700 - 1.5000 0.98 2693 148 0.3204 0.4031 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.206 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.812 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.89 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 1253 REMARK 3 ANGLE : 1.053 1670 REMARK 3 CHIRALITY : 0.056 186 REMARK 3 PLANARITY : 0.005 206 REMARK 3 DIHEDRAL : 16.397 520 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 7R7B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000257757. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23079 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 46.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 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 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: 2K5L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M DI-POTASSIUM PHOSPHATE, 2.2 M REMARK 280 AMMONIUM SULFATE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 46.28800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.77600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.28800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.77600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLN A 75 REMARK 465 GLU A 76 REMARK 465 GLN B 75 REMARK 465 GLU B 76 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 203 O HOH A 232 2.17 REMARK 500 O HOH A 201 O HOH B 218 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 46 -9.57 71.41 REMARK 500 LEU B 46 -6.41 73.17 REMARK 500 REMARK 500 REMARK: NULL 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 274 DISTANCE = 5.81 ANGSTROMS DBREF1 7R7B A 1 76 UNP A0A081U6Q6_BACFG DBREF2 7R7B A A0A081U6Q6 1 76 DBREF1 7R7B B 1 76 UNP A0A081U6Q6_BACFG DBREF2 7R7B B A0A081U6Q6 1 76 SEQRES 1 A 76 MET ARG LEU SER GLU LEU LYS THR GLY GLU LYS GLY VAL SEQRES 2 A 76 ILE VAL LYS VAL LEU GLY HIS GLY GLY PHE ARG LYS ARG SEQRES 3 A 76 ILE VAL GLU MET GLY PHE ILE LYS GLY LYS THR VAL GLU SEQRES 4 A 76 VAL LEU LEU ASN ALA PRO LEU LYS ASP PRO ILE LYS TYR SEQRES 5 A 76 LYS ILE MET GLY TYR GLU ILE SER LEU ARG ARG GLN GLU SEQRES 6 A 76 ALA ASP MET ILE GLU ILE ILE SER GLU GLN GLU SEQRES 1 B 76 MET ARG LEU SER GLU LEU LYS THR GLY GLU LYS GLY VAL SEQRES 2 B 76 ILE VAL LYS VAL LEU GLY HIS GLY GLY PHE ARG LYS ARG SEQRES 3 B 76 ILE VAL GLU MET GLY PHE ILE LYS GLY LYS THR VAL GLU SEQRES 4 B 76 VAL LEU LEU ASN ALA PRO LEU LYS ASP PRO ILE LYS TYR SEQRES 5 B 76 LYS ILE MET GLY TYR GLU ILE SER LEU ARG ARG GLN GLU SEQRES 6 B 76 ALA ASP MET ILE GLU ILE ILE SER GLU GLN GLU HET PO4 A 101 5 HET GOL A 102 6 HET PO4 B 101 5 HET GOL B 102 6 HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 PO4 2(O4 P 3-) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *150(H2 O) HELIX 1 AA1 ARG A 2 LEU A 6 5 5 HELIX 2 AA2 HIS A 20 MET A 30 1 11 HELIX 3 AA3 ARG A 62 ASP A 67 1 6 HELIX 4 AA4 ARG B 2 LEU B 6 5 5 HELIX 5 AA5 HIS B 20 MET B 30 1 11 HELIX 6 AA6 ARG B 62 ASP B 67 1 6 SHEET 1 AA1 5 TYR A 57 LEU A 61 0 SHEET 2 AA1 5 ILE A 50 ILE A 54 -1 N ILE A 50 O LEU A 61 SHEET 3 AA1 5 THR A 37 LEU A 42 -1 N GLU A 39 O LYS A 53 SHEET 4 AA1 5 LYS A 11 VAL A 17 -1 N GLY A 12 O VAL A 38 SHEET 5 AA1 5 ILE A 69 SER A 73 -1 O GLU A 70 N LYS A 16 SHEET 1 AA2 5 TYR B 57 LEU B 61 0 SHEET 2 AA2 5 ILE B 50 ILE B 54 -1 N TYR B 52 O ILE B 59 SHEET 3 AA2 5 THR B 37 LEU B 42 -1 N GLU B 39 O LYS B 53 SHEET 4 AA2 5 LYS B 11 VAL B 17 -1 N GLY B 12 O VAL B 38 SHEET 5 AA2 5 ILE B 69 SER B 73 -1 O GLU B 70 N LYS B 16 CISPEP 1 ASP A 48 PRO A 49 0 1.80 CISPEP 2 ASP B 48 PRO B 49 0 -2.10 CRYST1 92.576 29.552 67.430 90.00 128.89 90.00 C 1 2 1 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 0.010802 0.000000 0.008711 0.00000 SCALE2 0.000000 0.033839 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019052 0.00000