HEADER TRANSPORT PROTEIN 14-JUN-23 8PEK TITLE STRUCTURE OF THE DIMERIC, PERIPLASMIC DOMAIN OF EXBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIOPOLYMER TRANSPORT PROTEIN EXBD; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SERRATIA MARCESCENS; SOURCE 3 ORGANISM_TAXID: 615; SOURCE 4 GENE: EXBD, AN695_0216350, AR325_24260, BVG93_18405, BVG97_18665, SOURCE 5 C3R40_07870, CHR63_10945, DMW43_16865, FOT62_00910, HMI62_22190, SOURCE 6 HP475_23720; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30(A)+ KEYWDS TON, TONB-BINDING, EXBB-INTEGRATED, PERIPLASMIC, EXBB-EXBD, DIMER, KEYWDS 2 TRANSPORT PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.ZINKE,B.BARDIAUX,N.IZADI-PRUNEYRE REVDAT 2 01-MAY-24 8PEK 1 JRNL REVDAT 1 06-SEP-23 8PEK 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. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8PEK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131163. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.15 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.3 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 50 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 1.5 MM [U-100% REMARK 210 13C; U-100% 15N] PERIPLASMIC REMARK 210 DOMAIN OF EXBD FROM SERRATIA REMARK 210 MARCESCENS, 90% H2O/10% D2O; 50 REMARK 210 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 1.5 MM [U-100% REMARK 210 13C; U-100% 15N] PERIPLASMIC REMARK 210 DOMAIN OF EXBD FROM SERRATIA REMARK 210 MARCESCENS, 100% D2O; 50 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 2 MM [U-100% 13C; U- REMARK 210 100% 15N; U-95% 2H] PERIPLASMIC REMARK 210 DOMAIN OF EXBD FROM SERRATIA REMARK 210 MARCESCENS, 90% H2O/10% D2O; 50 REMARK 210 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 2 MM [U-100% REMARK 210 13C; U-100% 15N; U-95% 2H; REMARK 210 NATURAL ABUNDANCE] PERIPLASMIC REMARK 210 DOMAIN OF EXBD FROM SERRATIA REMARK 210 MARCESCENS, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D HN(CO)CA; 3D HNCO; REMARK 210 3D HN(CA)CO; 3D HNCACB; 3D REMARK 210 HN(COCA)CB; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 2D HBCBCGCDHD; 2D REMARK 210 HBCBCGCDCEHE; 2D 1H-15N TROSY; REMARK 210 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY AROMATIC; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D HNCO REMARK 210 HYDROGEN BOND DETECTION; 3D REMARK 210 DOUBLY-FILTERED 1H-13C NOESY; 3D REMARK 210 DOUBLY-FILTERED 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO; AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS ASSIGN 3.1, ARIA REMARK 210 2.3.3, CCPNMR ANALYSIS 2.5, REMARK 210 NMRPIPE 10.9, TALOS-N 4.12 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 7 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 SER A 42 REMARK 465 SER B 42 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 SER A 53 82.51 48.67 REMARK 500 1 PRO A 58 61.01 -69.90 REMARK 500 1 ARG A 59 81.86 54.25 REMARK 500 1 ALA A 96 -2.68 77.28 REMARK 500 1 ALA A 138 85.66 -151.84 REMARK 500 1 SER B 53 82.33 48.75 REMARK 500 1 PRO B 58 61.16 -69.90 REMARK 500 1 ARG B 59 81.78 54.16 REMARK 500 1 LYS B 62 79.90 -116.47 REMARK 500 1 ALA B 96 -2.29 76.97 REMARK 500 1 ALA B 138 85.72 -151.28 REMARK 500 2 SER A 53 108.20 69.10 REMARK 500 2 ARG A 59 80.35 52.11 REMARK 500 2 ALA A 96 -0.03 75.66 REMARK 500 2 SER B 53 108.51 68.97 REMARK 500 2 ARG B 59 80.66 52.56 REMARK 500 3 SER A 52 -73.94 67.45 REMARK 500 3 SER A 53 120.00 -169.55 REMARK 500 3 ARG A 59 81.62 54.65 REMARK 500 3 LYS A 62 78.55 -118.72 REMARK 500 3 SER B 52 -73.88 67.67 REMARK 500 3 SER B 53 119.75 -169.59 REMARK 500 3 ARG B 59 81.35 54.04 REMARK 500 3 LYS B 62 78.56 -118.99 REMARK 500 4 SER A 52 -89.80 65.44 REMARK 500 4 ARG A 59 80.19 53.78 REMARK 500 4 SER B 52 -90.13 65.50 REMARK 500 4 ARG B 59 80.16 53.61 REMARK 500 4 TYR B 127 96.37 -69.98 REMARK 500 5 SER A 53 75.74 56.57 REMARK 500 5 ALA A 54 -166.47 -125.23 REMARK 500 5 PRO A 58 48.91 -74.90 REMARK 500 5 ARG A 59 91.04 55.70 REMARK 500 5 TYR A 127 98.23 -69.52 REMARK 500 5 SER B 53 75.37 56.99 REMARK 500 5 ALA B 54 -166.70 -124.81 REMARK 500 5 PRO B 58 48.66 -75.00 REMARK 500 5 ARG B 59 90.72 55.93 REMARK 500 5 TYR B 127 98.14 -69.55 REMARK 500 6 SER A 53 137.58 70.89 REMARK 500 6 ALA A 54 -169.04 -173.85 REMARK 500 6 ARG A 59 80.56 52.07 REMARK 500 6 SER B 53 137.66 70.72 REMARK 500 6 ALA B 54 -168.99 -173.89 REMARK 500 6 ARG B 59 80.61 52.00 REMARK 500 7 SER A 53 102.01 64.75 REMARK 500 7 ARG A 59 82.07 55.39 REMARK 500 7 TYR A 127 99.88 -69.06 REMARK 500 7 SER B 53 101.58 65.25 REMARK 500 7 ARG B 59 82.32 55.73 REMARK 500 REMARK 500 THIS ENTRY HAS 69 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34826 RELATED DB: BMRB REMARK 900 STRUCTURE OF THE DIMERIC, PERIPLASMIC DOMAIN OF EXBD DBREF 8PEK A 43 140 UNP V5YUQ0 V5YUQ0_SERMA 43 140 DBREF 8PEK B 43 140 UNP V5YUQ0 V5YUQ0_SERMA 43 140 SEQADV 8PEK SER A 42 UNP V5YUQ0 EXPRESSION TAG SEQADV 8PEK SER B 42 UNP V5YUQ0 EXPRESSION TAG SEQRES 1 A 99 SER VAL ASP ILE ARG VAL ASP LEU PRO ALA SER SER ALA SEQRES 2 A 99 LYS PRO GLN PRO ARG PRO GLU LYS PRO VAL PHE LEU SER SEQRES 3 A 99 VAL LYS ALA ASP LYS GLN LEU TYR VAL GLY ASP GLN PRO SEQRES 4 A 99 VAL ASN ALA ASP GLN LEU THR SER VAL LEU ASP GLN ARG SEQRES 5 A 99 THR GLN ALA ASN LYS GLU THR THR ILE PHE PHE GLN ALA SEQRES 6 A 99 ASP LYS SER VAL ASP TYR GLU THR LEU MET SER VAL MET SEQRES 7 A 99 ASP THR LEU ARG LYS ALA GLY TYR LEU LYS VAL GLY LEU SEQRES 8 A 99 VAL GLY MET GLU GLY ALA ALA LYS SEQRES 1 B 99 SER VAL ASP ILE ARG VAL ASP LEU PRO ALA SER SER ALA SEQRES 2 B 99 LYS PRO GLN PRO ARG PRO GLU LYS PRO VAL PHE LEU SER SEQRES 3 B 99 VAL LYS ALA ASP LYS GLN LEU TYR VAL GLY ASP GLN PRO SEQRES 4 B 99 VAL ASN ALA ASP GLN LEU THR SER VAL LEU ASP GLN ARG SEQRES 5 B 99 THR GLN ALA ASN LYS GLU THR THR ILE PHE PHE GLN ALA SEQRES 6 B 99 ASP LYS SER VAL ASP TYR GLU THR LEU MET SER VAL MET SEQRES 7 B 99 ASP THR LEU ARG LYS ALA GLY TYR LEU LYS VAL GLY LEU SEQRES 8 B 99 VAL GLY MET GLU GLY ALA ALA LYS HELIX 1 AA1 ASN A 82 THR A 94 1 13 HELIX 2 AA2 ASP A 111 GLY A 126 1 16 HELIX 3 AA3 MET A 135 GLY A 137 5 3 HELIX 4 AA4 ASN B 82 THR B 94 1 13 HELIX 5 AA5 ASP B 111 GLY B 126 1 16 HELIX 6 AA6 MET B 135 GLY B 137 5 3 SHEET 1 AA112 GLN A 79 VAL A 81 0 SHEET 2 AA112 LEU A 74 VAL A 76 -1 N VAL A 76 O GLN A 79 SHEET 3 AA112 VAL A 64 VAL A 68 -1 N SER A 67 O TYR A 75 SHEET 4 AA112 ILE A 102 ALA A 106 1 O GLN A 105 N LEU A 66 SHEET 5 AA112 LYS A 129 VAL A 133 1 O GLY A 131 N ILE A 102 SHEET 6 AA112 ASP B 44 ASP B 48 -1 O VAL B 47 N VAL A 130 SHEET 7 AA112 ASP A 44 ASP A 48 -1 N ARG A 46 O ASP B 48 SHEET 8 AA112 LYS B 129 VAL B 133 -1 O VAL B 130 N VAL A 47 SHEET 9 AA112 ILE B 102 ALA B 106 1 N ILE B 102 O GLY B 131 SHEET 10 AA112 VAL B 64 VAL B 68 1 N LEU B 66 O GLN B 105 SHEET 11 AA112 LEU B 74 VAL B 76 -1 O TYR B 75 N SER B 67 SHEET 12 AA112 GLN B 79 VAL B 81 -1 O GLN B 79 N VAL B 76 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1