HEADER PROTEIN BINDING 13-DEC-13 2MII TITLE NMR STRUCTURE OF E. COLI LPOB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PENICILLIN-BINDING PROTEIN ACTIVATOR LPOB; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PBP ACTIVATOR LPOB; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 316385; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: YCFM, LPOB, ECDH10B_1177; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28LPOB KEYWDS LPOB, PBP1B ACTIVATOR, PEPTIDOGLYCAN SYNTHESIS, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.L.JEAN,A.J.F.EGAN,A.KOUMOUTSI,C.M.BOUGAULT,A.TYPAS,W.VOLLMER, AUTHOR 2 J.P.SIMORRE REVDAT 5 15-MAY-24 2MII 1 REMARK REVDAT 4 14-JUN-23 2MII 1 REMARK SEQADV REVDAT 3 25-JUN-14 2MII 1 JRNL REVDAT 2 18-JUN-14 2MII 1 JRNL REVDAT 1 21-MAY-14 2MII 0 JRNL AUTH A.J.EGAN,N.L.JEAN,A.KOUMOUTSI,C.M.BOUGAULT,J.BIBOY, JRNL AUTH 2 J.SASSINE,A.S.SOLOVYOVA,E.BREUKINK,A.TYPAS,W.VOLLMER, JRNL AUTH 3 J.P.SIMORRE JRNL TITL OUTER-MEMBRANE LIPOPROTEIN LPOB SPANS THE PERIPLASM TO JRNL TITL 2 STIMULATE THE PEPTIDOGLYCAN SYNTHASE PBP1B. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 8197 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 24821816 JRNL DOI 10.1073/PNAS.1400376111 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3.1, CNS 1.2, CNS REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), BRUNGER, REMARK 3 ADAMS, CLORE, GROS, NILGES AND READ (CNS), BRUNGER,ADAMS,CLORE, REMARK 3 DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, REMARK 3 RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MII COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000103654. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308.000 REMARK 210 PH : 5.000 REMARK 210 IONIC STRENGTH : 0.100 REMARK 210 PRESSURE : 1.000 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-100% 13C; U-100% 15N] REMARK 210 LPOB, 100.0 MM CH3COOH/CH3COONA REMARK 210 BUFFER, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D BEST-HNCACB; 3D REMARK 210 BEST-HN(CO)CACB; 3D HN(COCA)N(H); REMARK 210 2D PRO-HN(COCAN); 2D PRO- REMARK 210 IHN(CAN); 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D METHYL 1H-13C-CT- REMARK 210 HSQC; 2D 1H-15N HMQC OPTIMIZED REMARK 210 FOR HIS SIDECHAINS; 3D HCCH- REMARK 210 TOCSY; 3D H(CCO)NH; 3D C(CO)NH; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D METHYL 1H-13C NOESY; REMARK 210 HETERONUCLEAR 1H-15N NOE REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : VNMRS; US2 REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 2.2, TALOS+, REMARK 210 UNIO10' 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 : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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 ALA A 102 HG1 THR A 106 1.52 REMARK 500 H LEU A 178 O TRP A 188 1.53 REMARK 500 H GLY A 84 O LYS A 118 1.55 REMARK 500 O MET A 68 H VAL A 72 1.58 REMARK 500 O SER A 91 HG SER A 141 1.59 REMARK 500 O SER A 166 H THR A 173 1.60 REMARK 500 H VAL A 92 OG1 THR A 106 1.60 REMARK 500 O MET A 129 H GLN A 133 1.60 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 62 CE1 TYR A 62 CZ 0.149 REMARK 500 2 TYR A 62 CZ TYR A 62 CE2 -0.159 REMARK 500 18 TYR A 62 CE1 TYR A 62 CZ 0.133 REMARK 500 18 TYR A 62 CZ TYR A 62 CE2 -0.145 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 3 -166.73 62.32 REMARK 500 1 ARG A 8 76.79 61.31 REMARK 500 1 PRO A 10 -89.54 -58.48 REMARK 500 1 ALA A 11 -50.47 -179.04 REMARK 500 1 PRO A 18 42.19 -71.38 REMARK 500 1 ALA A 19 101.73 -168.96 REMARK 500 1 GLU A 21 -68.06 -137.10 REMARK 500 1 PRO A 31 37.21 -90.14 REMARK 500 1 GLU A 47 81.09 56.77 REMARK 500 1 GLN A 51 132.61 66.41 REMARK 500 1 ALA A 56 110.36 65.03 REMARK 500 1 PRO A 57 -177.00 -68.95 REMARK 500 1 ARG A 60 -150.32 -61.46 REMARK 500 1 THR A 96 -170.94 -51.05 REMARK 500 1 LEU A 136 -169.73 -64.92 REMARK 500 1 PRO A 138 1.35 -67.26 REMARK 500 1 SER A 141 166.33 75.78 REMARK 500 1 ALA A 171 88.89 -154.55 REMARK 500 1 GLN A 177 118.16 -170.57 REMARK 500 1 THR A 183 -36.97 -130.58 REMARK 500 2 HIS A 3 71.30 56.27 REMARK 500 2 GLU A 14 97.51 59.60 REMARK 500 2 PRO A 31 37.27 -81.66 REMARK 500 2 GLN A 42 129.43 70.14 REMARK 500 2 GLU A 47 76.96 50.55 REMARK 500 2 GLN A 51 -85.70 58.60 REMARK 500 2 PRO A 57 -177.84 -69.40 REMARK 500 2 ARG A 60 -150.28 -71.81 REMARK 500 2 THR A 96 -170.13 -51.40 REMARK 500 2 LEU A 136 -167.00 -67.25 REMARK 500 2 SER A 141 171.75 75.66 REMARK 500 2 ALA A 171 88.75 -154.78 REMARK 500 2 GLN A 177 119.26 -170.78 REMARK 500 2 THR A 183 -36.57 -130.64 REMARK 500 3 HIS A 3 132.75 73.06 REMARK 500 3 GLN A 7 109.53 63.56 REMARK 500 3 GLU A 14 89.91 67.95 REMARK 500 3 PRO A 20 -73.72 -80.35 REMARK 500 3 GLU A 21 63.17 -167.49 REMARK 500 3 PRO A 40 -175.91 -67.22 REMARK 500 3 GLU A 47 80.63 56.53 REMARK 500 3 PRO A 55 -93.06 -79.35 REMARK 500 3 ARG A 60 -158.84 -71.14 REMARK 500 3 THR A 96 -170.96 -52.00 REMARK 500 3 LEU A 136 -171.44 -66.93 REMARK 500 3 PRO A 138 0.44 -66.26 REMARK 500 3 SER A 141 168.95 73.52 REMARK 500 3 ALA A 171 89.07 -154.23 REMARK 500 3 GLN A 177 118.22 -170.78 REMARK 500 3 THR A 183 -36.61 -130.20 REMARK 500 REMARK 500 THIS ENTRY HAS 376 RAMACHANDRAN OUTLIERS. 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 PHE A 119 0.07 SIDE CHAIN REMARK 500 4 TYR A 162 0.07 SIDE CHAIN REMARK 500 5 TYR A 162 0.08 SIDE CHAIN REMARK 500 6 TYR A 162 0.08 SIDE CHAIN REMARK 500 7 TYR A 162 0.07 SIDE CHAIN REMARK 500 8 PHE A 119 0.07 SIDE CHAIN REMARK 500 8 TYR A 162 0.07 SIDE CHAIN REMARK 500 9 TYR A 162 0.06 SIDE CHAIN REMARK 500 17 TYR A 162 0.08 SIDE CHAIN REMARK 500 18 PHE A 119 0.08 SIDE CHAIN REMARK 500 19 TYR A 162 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19681 RELATED DB: BMRB DBREF 2MII A 5 197 UNP B1XA15 B1XA15_ECODH 21 213 SEQADV 2MII GLY A 1 UNP B1XA15 EXPRESSION TAG SEQADV 2MII SER A 2 UNP B1XA15 EXPRESSION TAG SEQADV 2MII HIS A 3 UNP B1XA15 EXPRESSION TAG SEQADV 2MII MET A 4 UNP B1XA15 EXPRESSION TAG SEQRES 1 A 197 GLY SER HIS MET VAL GLY GLN ARG GLU PRO ALA PRO VAL SEQRES 2 A 197 GLU GLU VAL LYS PRO ALA PRO GLU GLN PRO ALA GLU PRO SEQRES 3 A 197 GLN GLN PRO VAL PRO THR VAL PRO SER VAL PRO THR ILE SEQRES 4 A 197 PRO GLN GLN PRO GLY PRO ILE GLU HIS GLU ASP GLN THR SEQRES 5 A 197 ALA PRO PRO ALA PRO HIS ILE ARG HIS TYR ASP TRP ASN SEQRES 6 A 197 GLY ALA MET GLN PRO MET VAL SER LYS MET LEU GLY ALA SEQRES 7 A 197 ASP GLY VAL THR ALA GLY SER VAL LEU LEU VAL ASP SER SEQRES 8 A 197 VAL ASN ASN ARG THR ASN GLY SER LEU ASN ALA ALA GLU SEQRES 9 A 197 ALA THR GLU THR LEU ARG ASN ALA LEU ALA ASN ASN GLY SEQRES 10 A 197 LYS PHE THR LEU VAL SER ALA GLN GLN LEU SER MET ALA SEQRES 11 A 197 LYS GLN GLN LEU GLY LEU SER PRO GLN ASP SER LEU GLY SEQRES 12 A 197 THR ARG SER LYS ALA ILE GLY ILE ALA ARG ASN VAL GLY SEQRES 13 A 197 ALA HIS TYR VAL LEU TYR SER SER ALA SER GLY ASN VAL SEQRES 14 A 197 ASN ALA PRO THR LEU GLN MET GLN LEU MET LEU VAL GLN SEQRES 15 A 197 THR GLY GLU ILE ILE TRP SER GLY LYS GLY ALA VAL SER SEQRES 16 A 197 GLN GLN HELIX 1 1 TRP A 64 LEU A 76 1 13 HELIX 2 2 ASN A 101 GLY A 117 1 17 HELIX 3 3 GLN A 126 GLY A 135 1 10 HELIX 4 4 THR A 144 GLY A 156 1 13 SHEET 1 A 2 TYR A 62 ASP A 63 0 SHEET 2 A 2 SER A 195 GLN A 196 -1 O SER A 195 N ASP A 63 SHEET 1 B 5 PHE A 119 LEU A 121 0 SHEET 2 B 5 SER A 85 ASN A 94 1 N SER A 85 O THR A 120 SHEET 3 B 5 TYR A 159 SER A 166 1 O LEU A 161 N LEU A 88 SHEET 4 B 5 THR A 173 LEU A 180 -1 O GLN A 177 N TYR A 162 SHEET 5 B 5 ILE A 186 ALA A 193 -1 O GLY A 190 N MET 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 TER 2905 GLN A 197 ENDMDL MODEL 2 TER 2905 GLN A 197 ENDMDL MODEL 3 TER 2905 GLN A 197 ENDMDL MODEL 4 TER 2905 GLN A 197 ENDMDL MODEL 5 TER 2905 GLN A 197 ENDMDL MODEL 6 TER 2905 GLN A 197 ENDMDL MODEL 7 TER 2905 GLN A 197 ENDMDL MODEL 8 TER 2905 GLN A 197 ENDMDL MODEL 9 TER 2905 GLN A 197 ENDMDL MODEL 10 TER 2905 GLN A 197 ENDMDL MODEL 11 TER 2905 GLN A 197 ENDMDL MODEL 12 TER 2905 GLN A 197 ENDMDL MODEL 13 TER 2905 GLN A 197 ENDMDL MODEL 14 TER 2905 GLN A 197 ENDMDL MODEL 15 TER 2905 GLN A 197 ENDMDL MODEL 16 TER 2905 GLN A 197 ENDMDL MODEL 17 TER 2905 GLN A 197 ENDMDL MODEL 18 TER 2905 GLN A 197 ENDMDL MODEL 19 TER 2905 GLN A 197 ENDMDL MODEL 20 TER 2905 GLN A 197 ENDMDL MASTER 220 0 0 4 7 0 0 6 1456 1 0 16 END