HEADER TRANSFERASE 15-MAR-18 6FZK TITLE NMR STRUCTURE OF UB2H, REGULATORY DOMAIN OF PBP1B FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN 1B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PBP1B (108-200); COMPND 5 SYNONYM: PBP1B,MUREIN POLYMERASE; COMPND 6 EC: 2.4.1.129,3.4.16.4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; 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 UB2H DOMAIN OF PBP1B, REGULATORY DOMAIN, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.P.SIMORRE,R.C.MAYA MARTINEZ,C.BOUGAULT,A.J.F.EGAN,W.VOLLMER REVDAT 3 14-JUN-23 6FZK 1 REMARK REVDAT 2 08-MAY-19 6FZK 1 REMARK REVDAT 1 20-FEB-19 6FZK 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 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 6FZK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200009116. 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 : 200 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 500 UM [U-13C; U-15N] UB2H, 450 REMARK 210 UM [U-99% 15N] UB2H, 100 UM NOT REMARK 210 LABEL UB2H_LYS-OXYL, 90% H2O AND 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 : 600 MHZ; 700 MHZ; 850 MHZ; 950 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III 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: 7840 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 O ASN A 185 H ASN A 189 1.58 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 0.151 REMARK 500 2 TYR A 133 CZ TYR A 133 CE2 -0.141 REMARK 500 4 PHE A 175 CE1 PHE A 175 CZ 0.120 REMARK 500 5 TYR A 133 CE1 TYR A 133 CZ 0.116 REMARK 500 5 TYR A 133 CZ TYR A 133 CE2 -0.125 REMARK 500 6 TYR A 133 CE1 TYR A 133 CZ 0.104 REMARK 500 6 TYR A 133 CZ TYR A 133 CE2 -0.120 REMARK 500 8 PHE A 192 CE1 PHE A 192 CZ 0.125 REMARK 500 9 TYR A 133 CE1 TYR A 133 CZ 0.129 REMARK 500 9 TYR A 133 CZ TYR A 133 CE2 -0.125 REMARK 500 10 TYR A 133 CE1 TYR A 133 CZ 0.115 REMARK 500 10 TYR A 133 CZ TYR A 133 CE2 -0.126 REMARK 500 12 TYR A 133 CE1 TYR A 133 CZ 0.116 REMARK 500 12 TYR A 133 CZ TYR A 133 CE2 -0.123 REMARK 500 13 TYR A 133 CE1 TYR A 133 CZ 0.088 REMARK 500 13 TYR A 133 CZ TYR A 133 CE2 -0.101 REMARK 500 13 PHE A 159 CE1 PHE A 159 CZ 0.120 REMARK 500 14 TYR A 133 CE1 TYR A 133 CZ 0.090 REMARK 500 14 TYR A 133 CZ TYR A 133 CE2 -0.099 REMARK 500 16 TYR A 133 CE1 TYR A 133 CZ 0.112 REMARK 500 16 TYR A 133 CZ TYR A 133 CE2 -0.125 REMARK 500 16 PHE A 192 CE1 PHE A 192 CZ 0.123 REMARK 500 18 TYR A 133 CE1 TYR A 133 CZ 0.125 REMARK 500 18 TYR A 133 CZ TYR A 133 CE2 -0.139 REMARK 500 18 PHE A 192 CE1 PHE A 192 CZ 0.114 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 HIS A 92 -158.12 -91.00 REMARK 500 1 SER A 98 97.74 -68.07 REMARK 500 1 ARG A 103 -32.10 74.42 REMARK 500 1 ARG A 109 90.25 -17.26 REMARK 500 1 PRO A 115 139.00 -34.14 REMARK 500 1 ASP A 116 35.56 77.22 REMARK 500 1 THR A 140 97.89 -161.57 REMARK 500 1 GLN A 148 -60.80 -142.61 REMARK 500 1 ALA A 149 -92.43 -108.92 REMARK 500 1 ASN A 189 33.91 73.86 REMARK 500 1 PHE A 192 -166.02 -106.44 REMARK 500 2 HIS A 96 107.07 -55.41 REMARK 500 2 SER A 105 -44.19 72.89 REMARK 500 2 HIS A 106 43.10 -83.28 REMARK 500 2 ARG A 109 94.85 -53.08 REMARK 500 2 PRO A 115 146.30 -34.77 REMARK 500 2 THR A 118 79.33 -101.81 REMARK 500 2 GLN A 148 -74.99 -99.18 REMARK 500 2 ALA A 149 -46.59 -173.62 REMARK 500 2 ASP A 160 76.93 -110.90 REMARK 500 2 ASN A 189 36.47 75.53 REMARK 500 2 PHE A 192 -166.79 -116.91 REMARK 500 3 HIS A 93 89.77 62.16 REMARK 500 3 HIS A 96 -85.56 69.35 REMARK 500 3 PRO A 115 130.83 -35.76 REMARK 500 3 ASP A 116 45.47 73.71 REMARK 500 3 ALA A 149 -50.05 72.65 REMARK 500 3 ASN A 189 32.15 78.20 REMARK 500 4 HIS A 93 37.66 -88.23 REMARK 500 4 HIS A 94 90.83 69.86 REMARK 500 4 SER A 98 82.20 -69.53 REMARK 500 4 ARG A 103 96.11 -67.39 REMARK 500 4 SER A 105 -74.39 64.02 REMARK 500 4 MET A 107 -79.20 -73.39 REMARK 500 4 ARG A 109 80.74 14.15 REMARK 500 4 ASN A 112 106.73 -160.10 REMARK 500 4 PRO A 115 129.03 -36.75 REMARK 500 4 ASP A 116 50.10 75.41 REMARK 500 4 ALA A 149 -60.73 -163.36 REMARK 500 4 ARG A 156 92.97 -68.24 REMARK 500 4 ASN A 189 32.02 75.48 REMARK 500 4 PRO A 199 172.04 -44.91 REMARK 500 5 SER A 90 73.09 -104.00 REMARK 500 5 HIS A 91 108.83 67.20 REMARK 500 5 HIS A 94 54.29 -101.58 REMARK 500 5 ARG A 103 48.31 -152.46 REMARK 500 5 MET A 107 55.87 -102.57 REMARK 500 5 ARG A 109 80.28 10.31 REMARK 500 5 PRO A 115 149.79 -34.27 REMARK 500 5 ASP A 116 31.26 70.55 REMARK 500 REMARK 500 THIS ENTRY HAS 221 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 MET A 139 THR A 140 1 149.40 REMARK 500 PHE A 192 GLY A 193 1 -149.26 REMARK 500 PHE A 192 GLY A 193 3 148.00 REMARK 500 PHE A 192 GLY A 193 4 146.77 REMARK 500 GLY A 193 PHE A 194 6 145.09 REMARK 500 PHE A 192 GLY A 193 7 145.78 REMARK 500 PHE A 192 GLY A 193 8 148.34 REMARK 500 PHE A 192 GLY A 193 9 145.47 REMARK 500 PHE A 192 GLY A 193 10 147.14 REMARK 500 PHE A 192 GLY A 193 11 144.92 REMARK 500 PHE A 192 GLY A 193 12 -147.68 REMARK 500 PHE A 192 GLY A 193 13 145.52 REMARK 500 PHE A 192 GLY A 193 14 145.94 REMARK 500 PHE A 192 GLY A 193 15 -148.26 REMARK 500 PHE A 192 GLY A 193 16 146.59 REMARK 500 PHE A 192 GLY A 193 17 145.18 REMARK 500 PHE A 192 GLY A 193 18 146.04 REMARK 500 PHE A 192 GLY A 193 19 -149.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 TYR A 133 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES 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: 5HLD RELATED DB: PDB REMARK 900 E. COLI PBP1B IN COMPLEX WITH ACYL-CENTA AND MOENOMYCIN REMARK 900 RELATED ID: 5HLB RELATED DB: PDB REMARK 900 E. COLI PBP1B IN COMPLEX WITH ACYL-AZTREONAM AND MOENOMYCIN REMARK 900 RELATED ID: 5HLA RELATED DB: PDB REMARK 900 E. COLI PBP1B IN COMPLEX WITH ACYL-CEPHALEXIN AND MOENOMYCIN REMARK 900 RELATED ID: 34246 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF UB2H, REGULATORY DOMAIN OF PBP1B FROM E. COLI DBREF 6FZK A 108 200 UNP P02919 PBPB_ECOLI 108 200 SEQADV 6FZK MET A 87 UNP P02919 INITIATING METHIONINE SEQADV 6FZK GLY A 88 UNP P02919 EXPRESSION TAG SEQADV 6FZK SER A 89 UNP P02919 EXPRESSION TAG SEQADV 6FZK SER A 90 UNP P02919 EXPRESSION TAG SEQADV 6FZK HIS A 91 UNP P02919 EXPRESSION TAG SEQADV 6FZK HIS A 92 UNP P02919 EXPRESSION TAG SEQADV 6FZK HIS A 93 UNP P02919 EXPRESSION TAG SEQADV 6FZK HIS A 94 UNP P02919 EXPRESSION TAG SEQADV 6FZK HIS A 95 UNP P02919 EXPRESSION TAG SEQADV 6FZK HIS A 96 UNP P02919 EXPRESSION TAG SEQADV 6FZK SER A 97 UNP P02919 EXPRESSION TAG SEQADV 6FZK SER A 98 UNP P02919 EXPRESSION TAG SEQADV 6FZK GLY A 99 UNP P02919 EXPRESSION TAG SEQADV 6FZK LEU A 100 UNP P02919 EXPRESSION TAG SEQADV 6FZK VAL A 101 UNP P02919 EXPRESSION TAG SEQADV 6FZK PRO A 102 UNP P02919 EXPRESSION TAG SEQADV 6FZK ARG A 103 UNP P02919 EXPRESSION TAG SEQADV 6FZK GLY A 104 UNP P02919 EXPRESSION TAG SEQADV 6FZK SER A 105 UNP P02919 EXPRESSION TAG SEQADV 6FZK HIS A 106 UNP P02919 EXPRESSION TAG SEQADV 6FZK 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 MET A 124 THR A 131 1 8 SHEET 1 AA1 4 GLU A 144 VAL A 147 0 SHEET 2 AA1 4 SER A 151 ILE A 155 -1 O GLU A 153 N THR A 146 SHEET 3 AA1 4 ARG A 170 ASP A 176 -1 O LEU A 173 N ILE A 152 SHEET 4 AA1 4 HIS A 179 ASN A 185 -1 O HIS A 179 N ASP A 176 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