HEADER TRANSFERASE 29-MAR-18 6G5R TITLE STRUCTURE OF THE UB2H DOMAIN OF E.COLI PBP1B IN COMPLEX WITH LPOB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 1B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UB2H DOMAIN (108-200); COMPND 5 SYNONYM: PBP1B,MUREIN POLYMERASE; COMPND 6 EC: 2.4.1.129,3.4.16.4; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: UB2H IS A DOMAIN OF E. COLI OF PBP1B (RESIDUES 108- COMPND 9 200) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: MRCB, PBPF, PONB, B0149, JW0145; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS MUREIN POLYMERASE, COMPLEX, LPOB, PBP1B, E. COLI, TRANSPEPTIDASE, KEYWDS 2 GLYCOSYLTRANSFERASE, PEPTIDOGLICAN, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.P.SIMORRE,R.C.MAYA MARTINEZ,C.BOUGAULT REVDAT 3 14-JUN-23 6G5R 1 REMARK REVDAT 2 08-MAY-19 6G5R 1 REMARK REVDAT 1 20-FEB-19 6G5R 0 JRNL AUTH A.J.F.EGAN,R.MAYA-MARTINEZ,I.AYALA,C.M.BOUGAULT,M.BANZHAF, JRNL AUTH 2 E.BREUKINK,W.VOLLMER,J.P.SIMORRE JRNL TITL INDUCED CONFORMATIONAL CHANGES ACTIVATE THE PEPTIDOGLYCAN JRNL TITL 2 SYNTHASE PBP1B. JRNL REF MOL. MICROBIOL. V. 110 335 2018 JRNL REFN ESSN 1365-2958 JRNL PMID 30044025 JRNL DOI 10.1111/MMI.14082 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.T.KING,G.A.WASNEY,M.NOSELLA,A.FONG,N.C.STRYNADKA REMARK 1 TITL STRUCTURAL INSIGHTS INTO INHIBITION OF ESCHERICHIA COLI REMARK 1 TITL 2 PENICILLIN-BINDING PROTEIN 1B. REMARK 1 REF J. BIOL. CHEM. V. 292 979 2017 REMARK 1 REFN ESSN 1083-351X REMARK 1 PMID 27899450 REMARK 1 DOI 10.1074/JBC.M116.718403 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3, CNS 1.2 REMARK 3 AUTHORS : RIEPING W., HABECK M., BARDIAUX B., BERNARD A , REMARK 3 NILGES M. (ARIA), BRUNGER, ADAMS, CLORE, GROS, REMARK 3 NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6G5R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200009117. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 210 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 400 UM [U-13C; U-15N] UB2H REMARK 210 DOMAIN, 480 UM NONE LPOB, 90% REMARK 210 H2O AND 10% D2O; 450 UM [U-15N] REMARK 210 UB2H, 540 UM NONE LPOB, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D BESTROSY-HNCACB; 3D REMARK 210 BESTROSY-HN(CO)CACB; 2D 1H-13C REMARK 210 HSQC ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 850 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; AVANCE III; US2 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 2.4, TALOS+, REMARK 210 UNIO 2.0.2, NMRDRAW, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 750 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : 20 REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 2 TYR A 133 CE1 TYR A 133 CZ 0.106 REMARK 500 2 TYR A 133 CZ TYR A 133 CE2 -0.135 REMARK 500 3 TYR A 133 CE1 TYR A 133 CZ 0.139 REMARK 500 3 TYR A 133 CZ TYR A 133 CE2 -0.165 REMARK 500 4 TYR A 133 CE1 TYR A 133 CZ 0.090 REMARK 500 4 TYR A 133 CZ TYR A 133 CE2 -0.120 REMARK 500 5 TYR A 133 CE1 TYR A 133 CZ 0.138 REMARK 500 5 TYR A 133 CZ TYR A 133 CE2 -0.169 REMARK 500 6 TYR A 133 CE1 TYR A 133 CZ 0.140 REMARK 500 6 TYR A 133 CZ TYR A 133 CE2 -0.164 REMARK 500 10 TYR A 133 CE1 TYR A 133 CZ 0.100 REMARK 500 10 TYR A 133 CZ TYR A 133 CE2 -0.127 REMARK 500 13 TYR A 133 CE1 TYR A 133 CZ 0.114 REMARK 500 13 TYR A 133 CZ TYR A 133 CE2 -0.141 REMARK 500 14 TYR A 133 CE1 TYR A 133 CZ 0.106 REMARK 500 14 TYR A 133 CZ TYR A 133 CE2 -0.127 REMARK 500 14 PHE A 175 CE1 PHE A 175 CZ -0.159 REMARK 500 14 PHE A 175 CZ PHE A 175 CE2 0.175 REMARK 500 15 PHE A 175 CE1 PHE A 175 CZ -0.153 REMARK 500 15 PHE A 175 CZ PHE A 175 CE2 0.172 REMARK 500 16 TYR A 133 CE1 TYR A 133 CZ 0.078 REMARK 500 16 TYR A 133 CZ TYR A 133 CE2 -0.096 REMARK 500 17 TYR A 133 CE1 TYR A 133 CZ 0.089 REMARK 500 17 TYR A 133 CZ TYR A 133 CE2 -0.116 REMARK 500 18 TYR A 133 CE1 TYR A 133 CZ 0.125 REMARK 500 18 TYR A 133 CZ TYR A 133 CE2 -0.151 REMARK 500 19 TYR A 133 CE1 TYR A 133 CZ 0.127 REMARK 500 19 TYR A 133 CZ TYR A 133 CE2 -0.151 REMARK 500 20 PHE A 192 CE1 PHE A 192 CZ -0.130 REMARK 500 20 PHE A 192 CZ PHE A 192 CE2 0.160 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 MET A 107 -79.72 66.03 REMARK 500 1 GLN A 148 -87.54 -124.96 REMARK 500 1 ALA A 149 -84.53 -165.39 REMARK 500 1 GLU A 166 -170.68 -171.96 REMARK 500 1 ASN A 185 98.59 -59.94 REMARK 500 1 ASN A 189 43.78 36.38 REMARK 500 1 ARG A 190 -31.17 -150.55 REMARK 500 1 PHE A 192 -83.62 -87.94 REMARK 500 2 SER A 89 -89.36 60.67 REMARK 500 2 HIS A 92 -150.22 65.50 REMARK 500 2 HIS A 93 133.86 74.49 REMARK 500 2 HIS A 94 -63.95 70.75 REMARK 500 2 HIS A 95 -53.42 -161.51 REMARK 500 2 HIS A 96 -39.03 176.96 REMARK 500 2 SER A 97 -179.27 176.56 REMARK 500 2 VAL A 101 112.63 66.75 REMARK 500 2 PRO A 102 109.91 -59.97 REMARK 500 2 ARG A 109 178.32 65.29 REMARK 500 2 MET A 110 29.89 -147.43 REMARK 500 2 GLN A 132 52.73 77.10 REMARK 500 2 GLN A 148 -87.31 -132.46 REMARK 500 2 ALA A 149 -82.03 -160.43 REMARK 500 2 GLU A 166 -167.58 -168.71 REMARK 500 2 ASN A 185 101.09 -59.89 REMARK 500 2 ASN A 189 32.08 36.70 REMARK 500 2 ARG A 190 -66.81 -138.40 REMARK 500 3 HIS A 92 49.88 -83.38 REMARK 500 3 HIS A 93 83.63 57.19 REMARK 500 3 LEU A 100 112.19 65.37 REMARK 500 3 PRO A 102 83.27 -64.22 REMARK 500 3 MET A 110 26.28 -145.20 REMARK 500 3 GLN A 132 54.64 74.49 REMARK 500 3 GLN A 135 160.65 -49.73 REMARK 500 3 GLN A 148 -85.32 -152.95 REMARK 500 3 ALA A 149 -92.01 -145.48 REMARK 500 3 ASN A 185 98.64 -59.52 REMARK 500 3 ASN A 189 32.00 35.32 REMARK 500 3 ARG A 190 -62.29 -145.17 REMARK 500 3 GLN A 191 42.09 -75.23 REMARK 500 3 PHE A 192 -35.72 -157.15 REMARK 500 4 SER A 89 39.06 -144.16 REMARK 500 4 HIS A 92 103.72 69.78 REMARK 500 4 HIS A 94 59.33 -92.51 REMARK 500 4 HIS A 96 -69.27 -138.38 REMARK 500 4 SER A 98 -166.60 63.54 REMARK 500 4 MET A 110 31.12 -149.66 REMARK 500 4 GLU A 114 -171.20 -173.81 REMARK 500 4 PRO A 115 -175.93 -41.92 REMARK 500 4 ASP A 116 28.31 -43.39 REMARK 500 4 GLN A 132 55.26 72.68 REMARK 500 REMARK 500 THIS ENTRY HAS 280 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 115 ASP A 116 1 141.67 REMARK 500 PRO A 115 ASP A 116 2 138.20 REMARK 500 PRO A 115 ASP A 116 3 139.67 REMARK 500 PRO A 115 ASP A 116 7 -148.87 REMARK 500 PRO A 115 ASP A 116 8 140.09 REMARK 500 PRO A 115 ASP A 116 9 138.40 REMARK 500 PRO A 115 ASP A 116 11 139.42 REMARK 500 PRO A 115 ASP A 116 12 139.71 REMARK 500 PRO A 115 ASP A 116 14 141.56 REMARK 500 PRO A 115 ASP A 116 16 136.98 REMARK 500 PRO A 115 ASP A 116 17 138.65 REMARK 500 PRO A 115 ASP A 116 20 142.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5HL9 RELATED DB: PDB REMARK 900 E. COLI PBP1B IN COMPLEX WITH ACYL-AMPICILLIN AND MOENOMYCIN REMARK 900 RELATED ID: 3FWL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE FULL-LENGTH TRANSGLYCOSYLASE PBP1B FROM REMARK 900 ESCHERICHIA COLI REMARK 900 RELATED ID: 3VMA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE FULL-LENGTH TRANSGLYCOSYLASE PBP1B FROM REMARK 900 ESCHERICHIA COLI REMARK 900 RELATED ID: 5FGZ RELATED DB: PDB REMARK 900 E. COLI PBP1B IN COMPLEX WITH FPI-1465 REMARK 900 RELATED ID: 2MII RELATED DB: PDB REMARK 900 NMR STRUCTURE OF E. COLI LPOB REMARK 900 RELATED ID: 19681 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF E. COLI LPOB REMARK 900 RELATED ID: 4Q6Z RELATED DB: PDB REMARK 900 LPOB C-TERMINAL DOMAIN FROM ESCHERICHIA COLI REMARK 900 RELATED ID: 6FZK RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE UB2H DOMAIN OF E. COLI PBP1B REMARK 900 RELATED ID: 34255 RELATED DB: BMRB REMARK 900 STRUCTURE OF THE UB2H DOMAIN OF E.COLI PBP1B IN COMPLEX WITH LPOB DBREF 6G5R A 108 200 UNP P02919 PBPB_ECOLI 108 200 SEQADV 6G5R MET A 87 UNP P02919 INITIATING METHIONINE SEQADV 6G5R GLY A 88 UNP P02919 EXPRESSION TAG SEQADV 6G5R SER A 89 UNP P02919 EXPRESSION TAG SEQADV 6G5R SER A 90 UNP P02919 EXPRESSION TAG SEQADV 6G5R HIS A 91 UNP P02919 EXPRESSION TAG SEQADV 6G5R HIS A 92 UNP P02919 EXPRESSION TAG SEQADV 6G5R HIS A 93 UNP P02919 EXPRESSION TAG SEQADV 6G5R HIS A 94 UNP P02919 EXPRESSION TAG SEQADV 6G5R HIS A 95 UNP P02919 EXPRESSION TAG SEQADV 6G5R HIS A 96 UNP P02919 EXPRESSION TAG SEQADV 6G5R SER A 97 UNP P02919 EXPRESSION TAG SEQADV 6G5R SER A 98 UNP P02919 EXPRESSION TAG SEQADV 6G5R GLY A 99 UNP P02919 EXPRESSION TAG SEQADV 6G5R LEU A 100 UNP P02919 EXPRESSION TAG SEQADV 6G5R VAL A 101 UNP P02919 EXPRESSION TAG SEQADV 6G5R PRO A 102 UNP P02919 EXPRESSION TAG SEQADV 6G5R ARG A 103 UNP P02919 EXPRESSION TAG SEQADV 6G5R GLY A 104 UNP P02919 EXPRESSION TAG SEQADV 6G5R SER A 105 UNP P02919 EXPRESSION TAG SEQADV 6G5R HIS A 106 UNP P02919 EXPRESSION TAG SEQADV 6G5R MET A 107 UNP P02919 EXPRESSION TAG SEQRES 1 A 114 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 114 LEU VAL PRO ARG GLY SER HIS MET GLY ARG MET VAL ASN SEQRES 3 A 114 LEU GLU PRO ASP MET THR ILE SER LYS ASN GLU MET VAL SEQRES 4 A 114 LYS LEU LEU GLU ALA THR GLN TYR ARG GLN VAL SER LYS SEQRES 5 A 114 MET THR ARG PRO GLY GLU PHE THR VAL GLN ALA ASN SER SEQRES 6 A 114 ILE GLU MET ILE ARG ARG PRO PHE ASP PHE PRO ASP SER SEQRES 7 A 114 LYS GLU GLY GLN VAL ARG ALA ARG LEU THR PHE ASP GLY SEQRES 8 A 114 ASP HIS LEU ALA THR ILE VAL ASN MET GLU ASN ASN ARG SEQRES 9 A 114 GLN PHE GLY PHE PHE ARG LEU ASP PRO ARG HELIX 1 AA1 SER A 120 THR A 131 1 12 SHEET 1 AA1 4 THR A 146 VAL A 147 0 SHEET 2 AA1 4 SER A 151 ARG A 156 -1 O GLU A 153 N THR A 146 SHEET 3 AA1 4 VAL A 169 ASP A 176 -1 O LEU A 173 N ILE A 152 SHEET 4 AA1 4 HIS A 179 ASN A 185 -1 O THR A 182 N THR A 174 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