HEADER TRANSFERASE 24-OCT-11 4A52 TITLE NMR STRUCTURE OF THE IMIPENEM-ACYLATED L,D-TRANSPEPTIDASE FROM TITLE 2 BACILLUS SUBTILIS CAVEAT 4A52 IM2 A 1142 HAS WRONG CHIRALITY AT ATOM C5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE L, D-TRANSPEPTIDASE YKUD; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-164; COMPND 5 SYNONYM: SPORE PROTEIN YKUD, IMIPENEM-LDTBS; COMPND 6 EC: 2.-.-.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: PREP4GROESL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET2818 KEYWDS TRANSFERASE, PEPTIDOGLYCAN, ANTIBIOTIC RESISTANCE, CYSTEINE PROTEASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.LECOQ,J.SIMORRE,C.BOUGAULT,M.ARTHUR,J.HUGONNET,C.VECKERLE,O.PESSEY REVDAT 4 24-JAN-18 4A52 1 CAVEAT JRNL REMARK ATOM REVDAT 3 15-JAN-14 4A52 1 AUTHOR JRNL REVDAT 2 11-JUL-12 4A52 1 HETATM REVDAT 1 30-MAY-12 4A52 0 JRNL AUTH L.LECOQ,C.BOUGAULT,J.HUGONNET,C.VECKERLE,O.PESSEY,M.ARTHUR, JRNL AUTH 2 J.P.SIMORRE JRNL TITL DYNAMICS INDUCED BY BETA-LACTAM ANTIBIOTICS IN THE ACTIVE JRNL TITL 2 SITE OF BACILLUS SUBTILIS L,D-TRANSPEPTIDASE. JRNL REF STRUCTURE V. 20 850 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 22579252 JRNL DOI 10.1016/J.STR.2012.03.015 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT IN WATER AFTER 8 ITERATIONS. REMARK 4 REMARK 4 4A52 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1290050038. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0; 298.0; 298.0; 298.0 REMARK 210 PH : 6.5; 6.5; 6.5; 6.5 REMARK 210 IONIC STRENGTH : 0.15; 0.15; 0.15; 0.15 REMARK 210 PRESSURE : 1.0 ATM; 1.0 ATM; 1.0 ATM; 1.0 REMARK 210 ATM REMARK 210 SAMPLE CONTENTS : 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 13C-HSQC-NOESY; 1H-15N- HSQC; 1H REMARK 210 -13C-HSQC; 13C- HSQC-NOESY REMARK 210 METHYL SELECTIVE; 15N-HSQC-NOESY; REMARK 210 1H-15N- HMQC OPTIMIZED FOR REMARK 210 IMIDAZOLE RING OF HISTIDINES; REMARK 210 HNCO; HNCACB; 1H- 13C-HSQC REMARK 210 CENTERED ON AROMATICS; 13C-HSQC- REMARK 210 NOESY CENTERED ON AROMATICS REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.2, TALOS ANY ANY, UNIO 10, REMARK 210 NMRDRAW ANY ANY, NMRPIPE ANY ANY, REMARK 210 CCPNMR ANALYSIS 2.2 REMARK 210 METHOD USED : ITERATIVE STRUCTURE CALCULATION REMARK 210 WITH ARIA2.3 REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURE WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE 20 NMR STRUCTURES WERE DETERMINED USING TRIPLE- REMARK 210 RESONANCE NMR SPECTROSCOPY ON A 13C, 15N-LABELED LDTBS SAMPLE REMARK 210 INCUBATED WITH 2.5 EQUIVALENTS OF IMIPENEM ANTIBIOTIC. THESE REMARK 210 STRUCTURES WERE REFINED WITH RDCS, AND REFINED IN WATER WITHIN REMARK 210 CNS ARIA. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 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 HZ2 LYS A 140 O31 IM2 A 1142 1.48 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 13 TYR A 55 CE1 TYR A 55 CZ -0.082 REMARK 500 13 TYR A 55 CZ TYR A 55 CE2 0.090 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 PRO A 34 -9.05 -57.87 REMARK 500 1 LYS A 68 18.06 55.39 REMARK 500 1 ASN A 76 2.00 82.19 REMARK 500 1 LYS A 80 159.47 179.32 REMARK 500 1 ILE A 89 71.43 -158.19 REMARK 500 1 THR A 91 -154.96 -96.99 REMARK 500 1 GLN A 92 98.32 73.01 REMARK 500 1 ILE A 100 104.69 -59.76 REMARK 500 1 ASN A 106 100.36 -45.19 REMARK 500 1 PRO A 110 18.16 -63.64 REMARK 500 1 ALA A 113 -39.05 73.59 REMARK 500 1 GLN A 121 -107.04 45.08 REMARK 500 1 HIS A 122 49.83 -91.80 REMARK 500 1 LYS A 140 47.02 37.26 REMARK 500 1 ASN A 159 3.84 -61.56 REMARK 500 2 ARG A 2 -173.63 63.64 REMARK 500 2 GLN A 11 106.18 -50.55 REMARK 500 2 PRO A 34 -9.36 -57.60 REMARK 500 2 LYS A 88 -72.46 -98.26 REMARK 500 2 ILE A 89 -84.63 65.20 REMARK 500 2 LEU A 90 -106.30 -126.77 REMARK 500 2 GLN A 92 -66.69 -178.13 REMARK 500 2 THR A 93 89.47 51.76 REMARK 500 2 THR A 95 109.29 -58.01 REMARK 500 2 ASN A 102 -172.64 -172.41 REMARK 500 2 ASN A 106 105.72 -44.03 REMARK 500 2 PRO A 110 49.56 -67.15 REMARK 500 2 ALA A 113 -24.53 74.62 REMARK 500 2 SER A 139 -143.49 -84.00 REMARK 500 2 LYS A 140 114.79 69.44 REMARK 500 2 ASN A 159 0.06 -61.44 REMARK 500 3 ARG A 2 -177.18 63.81 REMARK 500 3 LYS A 80 160.19 179.98 REMARK 500 3 ILE A 89 -85.48 -119.11 REMARK 500 3 THR A 91 -61.62 -165.68 REMARK 500 3 GLN A 92 -68.17 -125.71 REMARK 500 3 THR A 93 67.52 61.47 REMARK 500 3 ASN A 102 -169.96 -172.36 REMARK 500 3 ASN A 106 104.85 -44.98 REMARK 500 3 PRO A 110 15.50 -61.98 REMARK 500 3 ALA A 113 -22.57 75.06 REMARK 500 3 SER A 119 -101.90 -85.61 REMARK 500 3 GLN A 121 125.43 71.00 REMARK 500 3 VAL A 138 -47.15 -154.78 REMARK 500 3 ASN A 159 -0.24 -59.63 REMARK 500 4 LYS A 68 16.94 59.97 REMARK 500 4 LYS A 80 154.71 179.26 REMARK 500 4 LYS A 88 -53.22 -171.18 REMARK 500 4 ILE A 89 -108.07 -105.03 REMARK 500 4 GLN A 92 -94.08 -74.00 REMARK 500 REMARK 500 THIS ENTRY HAS 284 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 13 TYR A 55 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IM2 A 1142 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y7M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE B. SUBTILIS YKUD PROTEIN AT 2 ARESOLUTION REMARK 900 RELATED ID: 3ZQD RELATED DB: PDB REMARK 900 B. SUBTILIS L,D-TRANSPEPTIDASE REMARK 900 RELATED ID: 4A1I RELATED DB: PDB REMARK 900 YKUD FROM B.SUBTILIS REMARK 900 RELATED ID: 4A1J RELATED DB: PDB REMARK 900 YKUD L,D-TRANSPEPTIDASE FROM B.SUBTILIS REMARK 900 RELATED ID: 4A1K RELATED DB: PDB REMARK 900 YKUD L,D-TRANSPEPTIDASE REMARK 900 RELATED ID: 18037 RELATED DB: BMRB DBREF 4A52 A 5 167 UNP O34816 YKUD_BACSU 2 164 SEQADV 4A52 GLY A 1 UNP O34816 EXPRESSION TAG SEQADV 4A52 ARG A 2 UNP O34816 EXPRESSION TAG SEQADV 4A52 LYS A 3 UNP O34816 EXPRESSION TAG SEQADV 4A52 LEU A 4 UNP O34816 EXPRESSION TAG SEQADV 4A52 GLY A 168 UNP O34816 EXPRESSION TAG SEQADV 4A52 SER A 169 UNP O34816 EXPRESSION TAG SEQADV 4A52 HIS A 170 UNP O34816 EXPRESSION TAG SEQADV 4A52 HIS A 171 UNP O34816 EXPRESSION TAG SEQADV 4A52 HIS A 172 UNP O34816 EXPRESSION TAG SEQADV 4A52 HIS A 173 UNP O34816 EXPRESSION TAG SEQADV 4A52 HIS A 174 UNP O34816 EXPRESSION TAG SEQADV 4A52 HIS A 175 UNP O34816 EXPRESSION TAG SEQRES 1 A 175 GLY ARG LYS LEU LEU THR TYR GLN VAL LYS GLN GLY ASP SEQRES 2 A 175 THR LEU ASN SER ILE ALA ALA ASP PHE ARG ILE SER THR SEQRES 3 A 175 ALA ALA LEU LEU GLN ALA ASN PRO SER LEU GLN ALA GLY SEQRES 4 A 175 LEU THR ALA GLY GLN SER ILE VAL ILE PRO GLY LEU PRO SEQRES 5 A 175 ASP PRO TYR THR ILE PRO TYR HIS ILE ALA VAL SER ILE SEQRES 6 A 175 GLY ALA LYS THR LEU THR LEU SER LEU ASN ASN ARG VAL SEQRES 7 A 175 MET LYS THR TYR PRO ILE ALA VAL GLY LYS ILE LEU THR SEQRES 8 A 175 GLN THR PRO THR GLY GLU PHE TYR ILE ILE ASN ARG GLN SEQRES 9 A 175 ARG ASN PRO GLY GLY PRO PHE GLY ALA TYR TRP LEU SER SEQRES 10 A 175 LEU SER LYS GLN HIS TYR GLY ILE HIS GLY THR ASN ASN SEQRES 11 A 175 PRO ALA SER ILE GLY LYS ALA VAL SER LYS GLY CYS ILE SEQRES 12 A 175 ARG MET HIS ASN LYS ASP VAL ILE GLU LEU ALA SER ILE SEQRES 13 A 175 VAL PRO ASN GLY THR ARG VAL THR ILE ASN ARG GLY SER SEQRES 14 A 175 HIS HIS HIS HIS HIS HIS HET IM2 A1142 38 HETNAM IM2 (5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-[(2-{[(E)- HETNAM 2 IM2 IMINOMETHYL]AMINO}ETHYL)SULFANYL]-4,5-DIHYDRO-1H- HETNAM 3 IM2 PYRROLE-2-CARBOXYLIC ACID HETSYN IM2 IMIPENEM, OPEN FORM; N-FORMIMIDOYL-THIENAMYCINE, OPEN HETSYN 2 IM2 FORM FORMUL 2 IM2 C12 H19 N3 O4 S HELIX 1 1 THR A 14 ALA A 20 1 7 HELIX 2 2 SER A 25 ALA A 32 1 8 HELIX 3 3 ASN A 33 ALA A 38 5 6 HELIX 4 4 HIS A 146 VAL A 157 1 12 SHEET 1 AA 2 LEU A 4 GLN A 8 0 SHEET 2 AA 2 SER A 45 ILE A 48 -1 O ILE A 46 N TYR A 7 SHEET 1 AB 5 ARG A 77 PRO A 83 0 SHEET 2 AB 5 THR A 69 LEU A 74 -1 O LEU A 70 N TYR A 82 SHEET 3 AB 5 HIS A 60 SER A 64 -1 N HIS A 60 O SER A 73 SHEET 4 AB 5 THR A 161 ASN A 166 1 O ARG A 162 N ILE A 61 SHEET 5 AB 5 GLU A 97 ILE A 100 -1 O PHE A 98 N VAL A 163 SHEET 1 AC 4 ASN A 102 ARG A 103 0 SHEET 2 AC 4 TRP A 115 SER A 117 -1 N SER A 117 O ASN A 102 SHEET 3 AC 4 GLY A 124 GLY A 127 -1 O ILE A 125 N LEU A 116 SHEET 4 AC 4 ILE A 143 MET A 145 1 O ILE A 143 N HIS A 126 LINK C7 IM2 A1142 SG CYS A 142 1555 1555 1.75 SITE 1 AC1 5 TRP A 115 HIS A 122 LYS A 140 CYS A 142 SITE 2 AC1 5 ARG A 144 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