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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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