HEADER MEMBRANE PROTEIN 06-JUN-23 8P9R TITLE STRUCTURE OF THE PERIPLASMIC DOMAIN OF EXBD FROM E. COLI IN COMPLEX TITLE 2 WITH TONB COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIOPOLYMER TRANSPORT PROTEIN EXBD; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROTEIN TONB; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: EXBD, B3005, JW2973; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 562 KEYWDS TON, TONB-BINDING, EXBB-INTEGRATED, PERIPLASMIC, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.ZINKE,A.MECHALY,M.LEJEUNE,A.HAOUZ,N.IZADI-PRUNEYRE REVDAT 2 01-MAY-24 8P9R 1 JRNL REVDAT 1 06-SEP-23 8P9R 0 JRNL AUTH M.ZINKE,M.LEJEUNE,A.MECHALY,B.BARDIAUX,I.G.BONECA, JRNL AUTH 2 P.DELEPELAIRE,N.IZADI-PRUNEYRE JRNL TITL TON MOTOR CONFORMATIONAL SWITCH AND PEPTIDOGLYCAN ROLE IN JRNL TITL 2 BACTERIAL NUTRIENT UPTAKE. JRNL REF NAT COMMUN V. 15 331 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38184686 JRNL DOI 10.1038/S41467-023-44606-Z REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.ZINKE,M.LEJEUNE,A.MECHALY,B.BARDIAUX,I.G.BONECA, REMARK 1 AUTH 2 P.DELEPELAIRE,N.IZADI-PRUNEYRE REMARK 1 TITL TON MOTOR CONFORMATIONAL SWITCH AND PEPTIDOGLYCAN ROLE IN REMARK 1 TITL 2 BACTERIAL NUTRIENT UPTAKE. REMARK 1 REF BIORXIV 2023 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 37609138 REMARK 1 DOI 10.1101/2023.08.11.552980 REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 23622 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1181 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 30.6400 - 3.0400 1.00 2847 150 0.1917 0.2122 REMARK 3 2 3.0400 - 2.4100 1.00 2832 149 0.2211 0.2606 REMARK 3 3 2.4100 - 2.1100 1.00 2797 148 0.2148 0.2605 REMARK 3 4 2.1100 - 1.9200 1.00 2814 148 0.2169 0.2225 REMARK 3 5 1.9100 - 1.7800 1.00 2780 146 0.2306 0.2521 REMARK 3 6 1.7800 - 1.6700 1.00 2800 147 0.2262 0.2766 REMARK 3 7 1.6700 - 1.5900 1.00 2782 146 0.2448 0.2767 REMARK 3 8 1.5900 - 1.5200 1.00 2789 147 0.3263 0.3696 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.750 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 NULL REMARK 3 ANGLE : 1.048 NULL REMARK 3 CHIRALITY : 0.065 203 REMARK 3 PLANARITY : 0.006 205 REMARK 3 DIHEDRAL : 9.091 163 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|2-75 } REMARK 3 ORIGIN FOR THE GROUP (A): 14.0937 4.9836 2.5930 REMARK 3 T TENSOR REMARK 3 T11: 0.2384 T22: 0.1961 REMARK 3 T33: 0.1874 T12: -0.0172 REMARK 3 T13: 0.0318 T23: -0.0276 REMARK 3 L TENSOR REMARK 3 L11: 3.3010 L22: 4.3717 REMARK 3 L33: 3.0584 L12: -1.1231 REMARK 3 L13: -1.0690 L23: 1.7921 REMARK 3 S TENSOR REMARK 3 S11: 0.0141 S12: 0.1634 S13: 0.1050 REMARK 3 S21: -0.3265 S22: 0.0229 S23: -0.0241 REMARK 3 S31: -0.1861 S32: -0.1588 S33: -0.0402 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { E|7-15 } REMARK 3 ORIGIN FOR THE GROUP (A): 18.3217 -6.4161 -1.0082 REMARK 3 T TENSOR REMARK 3 T11: 0.3628 T22: 0.3306 REMARK 3 T33: 0.4438 T12: -0.1108 REMARK 3 T13: 0.0724 T23: -0.0601 REMARK 3 L TENSOR REMARK 3 L11: 4.6305 L22: 4.3234 REMARK 3 L33: 8.0771 L12: -1.4440 REMARK 3 L13: 2.8473 L23: -1.3720 REMARK 3 S TENSOR REMARK 3 S11: -0.3466 S12: 0.3312 S13: -0.3158 REMARK 3 S21: -0.1101 S22: -0.0437 S23: -0.6191 REMARK 3 S31: -0.5683 S32: 0.9987 S33: 0.2074 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { B|3-75 } REMARK 3 ORIGIN FOR THE GROUP (A): 29.7272 -10.4256 -3.6772 REMARK 3 T TENSOR REMARK 3 T11: 0.1653 T22: 0.2120 REMARK 3 T33: 0.1551 T12: -0.0269 REMARK 3 T13: 0.0294 T23: -0.0396 REMARK 3 L TENSOR REMARK 3 L11: 4.1143 L22: 3.3058 REMARK 3 L33: 3.2149 L12: -1.4996 REMARK 3 L13: -1.5495 L23: 0.9634 REMARK 3 S TENSOR REMARK 3 S11: 0.0880 S12: -0.2850 S13: 0.1486 REMARK 3 S21: 0.1611 S22: -0.0291 S23: -0.0930 REMARK 3 S31: 0.0807 S32: 0.1283 S33: -0.0213 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 8P9R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292130908. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-23 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3799 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46421 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 39.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05850 REMARK 200 FOR THE DATA SET : 21.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.78400 REMARK 200 FOR SHELL : 2.450 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 %W/V GLYCEROL, 3M AMMONIUM SULFATE, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 31.97000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.98500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.95500 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, 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 SER A 60 REMARK 465 GLU A 135 REMARK 465 GLU A 136 REMARK 465 THR A 137 REMARK 465 ALA A 138 REMARK 465 LYS A 139 REMARK 465 ALA A 140 REMARK 465 LYS A 141 REMARK 465 LYS C 40 REMARK 465 LYS C 41 REMARK 465 ALA C 42 REMARK 465 PRO C 52 REMARK 465 ALA C 53 REMARK 465 ASP C 54 REMARK 465 LEU C 55 REMARK 465 GLU C 56 REMARK 465 PRO C 57 REMARK 465 PRO C 58 REMARK 465 GLN C 59 REMARK 465 ALA C 60 REMARK 465 LYS C 61 REMARK 465 LYS C 62 REMARK 465 SER B 60 REMARK 465 GLU B 61 REMARK 465 GLU B 135 REMARK 465 GLU B 136 REMARK 465 THR B 137 REMARK 465 ALA B 138 REMARK 465 LYS B 139 REMARK 465 ALA B 140 REMARK 465 LYS B 141 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 GLU A 61 CG CD OE1 OE2 DBREF 8P9R A 61 141 UNP P0ABV2 EXBD_ECOLI 61 141 DBREF 8P9R C 40 62 UNP P02929 TONB_ECOLI 40 62 DBREF 8P9R B 61 141 UNP P0ABV2 EXBD_ECOLI 61 141 SEQADV 8P9R SER A 60 UNP P0ABV2 EXPRESSION TAG SEQADV 8P9R LYS C 40 UNP P02929 ALA 40 CONFLICT SEQADV 8P9R LYS C 41 UNP P02929 PRO 41 CONFLICT SEQADV 8P9R LYS C 61 UNP P02929 VAL 61 CONFLICT SEQADV 8P9R LYS C 62 UNP P02929 GLN 62 CONFLICT SEQADV 8P9R SER B 60 UNP P0ABV2 EXPRESSION TAG SEQRES 1 A 82 SER GLU LYS PRO VAL TYR LEU SER VAL LYS ALA ASP ASN SEQRES 2 A 82 SER MET PHE ILE GLY ASN ASP PRO VAL THR ASP GLU THR SEQRES 3 A 82 MET ILE THR ALA LEU ASN ALA LEU THR GLU GLY LYS LYS SEQRES 4 A 82 ASP THR THR ILE PHE PHE ARG ALA ASP LYS THR VAL ASP SEQRES 5 A 82 TYR GLU THR LEU MET LYS VAL MET ASP THR LEU HIS GLN SEQRES 6 A 82 ALA GLY TYR LEU LYS ILE GLY LEU VAL GLY GLU GLU THR SEQRES 7 A 82 ALA LYS ALA LYS SEQRES 1 C 23 LYS LYS ALA GLN PRO ILE SER VAL THR MET VAL THR PRO SEQRES 2 C 23 ALA ASP LEU GLU PRO PRO GLN ALA LYS LYS SEQRES 1 B 82 SER GLU LYS PRO VAL TYR LEU SER VAL LYS ALA ASP ASN SEQRES 2 B 82 SER MET PHE ILE GLY ASN ASP PRO VAL THR ASP GLU THR SEQRES 3 B 82 MET ILE THR ALA LEU ASN ALA LEU THR GLU GLY LYS LYS SEQRES 4 B 82 ASP THR THR ILE PHE PHE ARG ALA ASP LYS THR VAL ASP SEQRES 5 B 82 TYR GLU THR LEU MET LYS VAL MET ASP THR LEU HIS GLN SEQRES 6 B 82 ALA GLY TYR LEU LYS ILE GLY LEU VAL GLY GLU GLU THR SEQRES 7 B 82 ALA LYS ALA LYS FORMUL 4 HOH *90(H2 O) HELIX 1 AA1 THR A 85 GLU A 95 1 11 HELIX 2 AA2 ASP A 111 ALA A 125 1 15 HELIX 3 AA3 THR B 85 GLU B 95 1 11 HELIX 4 AA4 ASP B 111 ALA B 125 1 15 SHEET 1 AA1 6 ASP A 79 VAL A 81 0 SHEET 2 AA1 6 MET A 74 ILE A 76 -1 N ILE A 76 O ASP A 79 SHEET 3 AA1 6 VAL A 64 VAL A 68 -1 N SER A 67 O PHE A 75 SHEET 4 AA1 6 ILE A 102 ALA A 106 1 O PHE A 103 N VAL A 64 SHEET 5 AA1 6 ILE A 130 VAL A 133 1 O VAL A 133 N PHE A 104 SHEET 6 AA1 6 THR C 48 VAL C 50 1 O THR C 48 N LEU A 132 SHEET 1 AA2 6 ILE C 45 SER C 46 0 SHEET 2 AA2 6 ILE B 130 LEU B 132 -1 O LEU B 132 N ILE C 45 SHEET 3 AA2 6 ILE B 102 ALA B 106 1 N PHE B 104 O GLY B 131 SHEET 4 AA2 6 VAL B 64 VAL B 68 1 N LEU B 66 O PHE B 103 SHEET 5 AA2 6 MET B 74 ILE B 76 -1 O PHE B 75 N SER B 67 SHEET 6 AA2 6 ASP B 79 VAL B 81 -1 O ASP B 79 N ILE B 76 CRYST1 49.360 49.360 63.940 90.00 90.00 90.00 P 41 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 0.020259 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020259 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015640 0.00000