HEADER TRANSFERASE 14-DEC-12 3ZG4 TITLE NMR STRUCTURE OF THE CATALYTIC DOMAIN FROM E. FAECIUM L,D- TITLE 2 TRANSPEPTIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ERFK/YBIS/YCFS/YNHG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 340-465; COMPND 5 SYNONYM: ERFK/YBIS/YCFS/YNHG FAMILY PROTEIN, LDTFM; COMPND 6 EC: 2.3.2.12; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECIUM; SOURCE 3 ORGANISM_TAXID: 1352; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PETTEV KEYWDS TRANSFERASE, TRANSPEPTIDATION, PEPTIDOGLYCAN BIOSYNTHESIS, ANTIBIOTIC KEYWDS 2 RESISTANCE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.LECOQ,V.DUBEE,S.TRIBOULET,C.BOUGAULT,J.E.HUGONNET,M.ARTHUR, AUTHOR 2 J.P.SIMORRE REVDAT 4 14-JUN-23 3ZG4 1 REMARK REVDAT 3 23-JUN-21 3ZG4 1 REMARK ATOM REVDAT 2 28-AUG-13 3ZG4 1 JRNL REVDAT 1 24-APR-13 3ZG4 0 JRNL AUTH L.LECOQ,V.DUBEE,S.TRIBOULET,C.BOUGAULT,J.E.HUGONNET, JRNL AUTH 2 M.ARTHUR,J.P.SIMORRE JRNL TITL THE STRUCTURE OF ENTEROCOCCUS FAECIUM L,D---TRANSPEPTIDASE JRNL TITL 2 ACYLATED BY ERTAPENEM PROVIDES INSIGHT INTO THE INACTIVATION JRNL TITL 3 MECHANISM. JRNL REF ACS CHEM.BIOL. V. 8 1140 2013 JRNL REFN ISSN 1554-8929 JRNL PMID 23574509 JRNL DOI 10.1021/CB4001603 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 3ZG4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1290055125. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 300 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 10% WATER/90% D2O; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-15N-HSQC; 1H-13C-HSQC REMARK 210 CENTERED ON ALIPHATICS; 1H-15N- REMARK 210 HMQC DETECTING 2J; 3J COUPLINGS REMARK 210 IN HISTIDINES IMIDAZOLE RING; 1H- REMARK 210 15N-HSQC DETECTING 1J COUPLING REMARK 210 IN HISTIDINES IMIDAZOLE RING; 3D- REMARK 210 15N- NOESY-HSQC; HNCO; 3D-13C- REMARK 210 NOESY-HSQC CENTERED ON REMARK 210 ALIPHATICS; 1H-13C-HSQC CENTERED REMARK 210 ON AROMATICS; 3D- 13C-NOESY-HSQC REMARK 210 CENTERED ON AROMATICS REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : DIRECT DRIVE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UNIO 10, TALOS, CCPNMR ANALYSIS REMARK 210 ANALYSIS REMARK 210 METHOD USED : ARIA2.3 REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1700 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TOTAL 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 LDTFM SAMPLE. REMARK 210 THESE STRUCTURES WERE REFINED IN WATER USING CNS1.2 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 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 TYR A 356 H ALA A 363 1.52 REMARK 500 OD1 ASP A 348 H ASN A 351 1.59 REMARK 500 H LYS A 372 O SER A 439 1.59 REMARK 500 O GLU A 388 H TRP A 410 1.59 REMARK 500 O GLU A 346 H TRP A 355 1.59 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 339 94.40 -174.61 REMARK 500 1 MET A 340 179.68 77.53 REMARK 500 1 GLN A 352 72.67 36.09 REMARK 500 1 PRO A 373 -28.82 -36.12 REMARK 500 1 ALA A 379 121.93 69.35 REMARK 500 1 ASN A 397 179.05 -51.85 REMARK 500 1 ASP A 432 100.53 -56.36 REMARK 500 2 MET A 340 -178.29 71.71 REMARK 500 2 GLN A 352 71.85 38.16 REMARK 500 2 PRO A 373 -32.89 -34.13 REMARK 500 2 ALA A 379 121.56 68.69 REMARK 500 2 ASN A 397 -179.45 -54.31 REMARK 500 2 ASP A 432 101.13 -54.77 REMARK 500 2 LYS A 459 155.08 -47.09 REMARK 500 3 HIS A 339 84.56 59.21 REMARK 500 3 MET A 340 -175.43 76.47 REMARK 500 3 GLN A 352 68.96 34.30 REMARK 500 3 PRO A 373 -32.68 -34.17 REMARK 500 3 ALA A 379 122.58 69.48 REMARK 500 3 ASN A 397 -179.65 -50.85 REMARK 500 3 ASP A 432 100.60 -51.08 REMARK 500 3 LYS A 459 153.43 -45.26 REMARK 500 4 MET A 340 172.98 79.48 REMARK 500 4 GLN A 352 73.14 38.87 REMARK 500 4 PRO A 373 -31.84 -33.49 REMARK 500 4 ALA A 379 123.22 69.36 REMARK 500 4 ASN A 397 -178.83 -52.77 REMARK 500 4 ASP A 432 100.33 -51.76 REMARK 500 4 HIS A 440 68.38 -101.21 REMARK 500 5 MET A 340 176.53 -54.46 REMARK 500 5 GLN A 352 71.25 35.94 REMARK 500 5 PRO A 373 -31.91 -36.02 REMARK 500 5 ALA A 379 124.25 67.05 REMARK 500 5 ASN A 397 -178.18 -55.40 REMARK 500 5 ASP A 432 100.62 -54.92 REMARK 500 5 LYS A 459 154.42 -46.21 REMARK 500 6 MET A 340 -173.58 63.78 REMARK 500 6 GLU A 341 -5.69 -144.37 REMARK 500 6 TYR A 344 -169.81 -164.66 REMARK 500 6 GLN A 352 69.48 38.01 REMARK 500 6 PRO A 373 -31.19 -37.95 REMARK 500 6 ALA A 379 122.79 70.64 REMARK 500 6 ASN A 397 179.29 -51.62 REMARK 500 6 ASP A 432 101.50 -55.04 REMARK 500 6 LYS A 459 154.24 -45.32 REMARK 500 7 MET A 340 178.95 69.09 REMARK 500 7 PRO A 373 -31.81 -35.11 REMARK 500 7 ALA A 379 122.87 67.66 REMARK 500 7 ASN A 397 179.97 -54.29 REMARK 500 7 ASP A 432 100.73 -55.56 REMARK 500 REMARK 500 THIS ENTRY HAS 140 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 GLY A 431 ASP A 432 1 -147.75 REMARK 500 GLY A 431 ASP A 432 2 -145.82 REMARK 500 GLY A 431 ASP A 432 5 -148.05 REMARK 500 GLY A 431 ASP A 432 6 -146.66 REMARK 500 GLY A 431 ASP A 432 7 -147.60 REMARK 500 GLY A 431 ASP A 432 9 -146.11 REMARK 500 GLY A 431 ASP A 432 10 -145.67 REMARK 500 GLY A 431 ASP A 432 11 -146.89 REMARK 500 GLY A 431 ASP A 432 12 -146.36 REMARK 500 GLY A 431 ASP A 432 13 -146.44 REMARK 500 GLY A 431 ASP A 432 14 -146.68 REMARK 500 GLY A 431 ASP A 432 15 -147.20 REMARK 500 GLY A 431 ASP A 432 16 -146.31 REMARK 500 GLY A 431 ASP A 432 17 -145.78 REMARK 500 GLY A 431 ASP A 432 19 -149.87 REMARK 500 GLY A 431 ASP A 432 20 -147.48 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 4 TYR A 356 0.05 SIDE CHAIN REMARK 500 5 TYR A 356 0.06 SIDE CHAIN REMARK 500 7 TYR A 356 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZGP RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE CATALYTIC DOMAIN FROM E. FAECIUM L,D- REMARK 900 TRANSPEPTIDASE ACYLATED BY ERTAPENEM REMARK 900 RELATED ID: 18900 RELATED DB: BMRB DBREF 3ZG4 A 340 465 UNP Q3Y185 Q3Y185_ENTFC 340 465 SEQADV 3ZG4 GLY A 338 UNP Q3Y185 EXPRESSION TAG SEQADV 3ZG4 HIS A 339 UNP Q3Y185 EXPRESSION TAG SEQADV 3ZG4 MET A 340 UNP Q3Y185 EXPRESSION TAG SEQRES 1 A 129 GLY HIS MET GLU ASP THR TYR ILE GLU VAL ASP LEU GLU SEQRES 2 A 129 ASN GLN HIS MET TRP TYR TYR LYS ASP GLY LYS VAL ALA SEQRES 3 A 129 LEU GLU THR ASP ILE VAL SER GLY LYS PRO THR THR PRO SEQRES 4 A 129 THR PRO ALA GLY VAL PHE TYR VAL TRP ASN LYS GLU GLU SEQRES 5 A 129 ASP ALA THR LEU LYS GLY THR ASN ASP ASP GLY THR PRO SEQRES 6 A 129 TYR GLU SER PRO VAL ASN TYR TRP MET PRO ILE ASP TRP SEQRES 7 A 129 THR GLY VAL GLY ILE HIS ASP SER ASP TRP GLN PRO GLU SEQRES 8 A 129 TYR GLY GLY ASP LEU TRP LYS THR ARG GLY SER HIS GLY SEQRES 9 A 129 CYS ILE ASN THR PRO PRO SER VAL MET LYS GLU LEU PHE SEQRES 10 A 129 GLY MET VAL GLU LYS GLY THR PRO VAL LEU VAL PHE HELIX 1 1 LEU A 433 GLY A 438 1 6 HELIX 2 2 PRO A 447 VAL A 457 1 11 SHEET 1 AA 3 THR A 343 ASP A 348 0 SHEET 2 AA 3 GLN A 352 LYS A 358 -1 O HIS A 353 N ASP A 348 SHEET 3 AA 3 LYS A 361 ASP A 367 -1 O LYS A 361 N LYS A 358 SHEET 1 AB 2 VAL A 381 VAL A 384 0 SHEET 2 AB 2 THR A 461 VAL A 465 -1 O VAL A 463 N PHE A 382 SHEET 1 AC 4 LYS A 387 GLU A 389 0 SHEET 2 AC 4 TYR A 409 PRO A 412 -1 O TRP A 410 N GLU A 388 SHEET 3 AC 4 GLY A 419 ASP A 422 -1 O ILE A 420 N MET A 411 SHEET 4 AC 4 ILE A 443 THR A 445 1 O ILE A 443 N HIS A 421 SHEET 1 AD 2 THR A 392 THR A 396 0 SHEET 2 AD 2 PRO A 402 PRO A 406 -1 O TYR A 403 N GLY A 395 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