HEADER TRANSFERASE 21-APR-15 4ZFQ TITLE STRUCTURE OF M. TUBERCULOSIS (3,3) L,D-TRANSPEPTIDASE, LDTMT5. TITLE 2 (MEROPENEN-ADDUCT FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: L,D-TRANSPEPTIDASE 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LDT 5,LDT(MT5); COMPND 5 EC: 2.3.2.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN CDC 1551 / SOURCE 3 OSHKOSH); SOURCE 4 ORGANISM_TAXID: 83331; SOURCE 5 STRAIN: CDC 1551 / OSHKOSH; SOURCE 6 GENE: MT0501; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PEPTIDOGLYCAN LINKAGE, CELL WALL BIOSYNTHESIS, CARBAPENEMS, KEYWDS 2 MYCOBATERIUM TUBERCULOSIS, L.D-TRANSPEPTIDASES, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.BASTA,A.GHOSH,G.LAMICHHANE,M.A.BIANCHET REVDAT 5 27-SEP-23 4ZFQ 1 REMARK REVDAT 4 02-FEB-22 4ZFQ 1 COMPND JRNL REMARK HETNAM REVDAT 4 2 1 HETSYN LINK REVDAT 3 28-OCT-15 4ZFQ 1 JRNL REVDAT 2 09-SEP-15 4ZFQ 1 JRNL REVDAT 1 02-SEP-15 4ZFQ 0 JRNL AUTH L.A.BRAMMER BASTA,A.GHOSH,Y.PAN,J.JAKONCIC,E.P.LLOYD, JRNL AUTH 2 C.A.TOWNSEND,G.LAMICHHANE,M.A.BIANCHET JRNL TITL LOSS OF A FUNCTIONALLY AND STRUCTURALLY DISTINCT JRNL TITL 2 LD-TRANSPEPTIDASE, LDTMT5, COMPROMISES CELL WALL INTEGRITY JRNL TITL 3 IN MYCOBACTERIUM TUBERCULOSIS. JRNL REF J.BIOL.CHEM. V. 290 25670 2015 JRNL REFN ESSN 1083-351X JRNL PMID 26304120 JRNL DOI 10.1074/JBC.M115.660753 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.B.ERDEMLI,R.GUPTA,W.R.BISHAI,G.LAMICHHANE,L.M.AMZEL, REMARK 1 AUTH 2 M.A.BIANCHET REMARK 1 TITL TARGETING THE CELL WALL OF MYCOBACTERIUM TUBERCULOSIS: REMARK 1 TITL 2 STRUCTURE AND MECHANISM OF L,D-TRANSPEPTIDASE 2. REMARK 1 REF STRUCTURE V. 20 2103 2012 REMARK 1 REFN ISSN 1878-4186 REMARK 1 PMID 23103390 REMARK 1 DOI 10.1016/J.STR.2012.09.016 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 14486 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 734 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.0460 - 4.7807 1.00 2939 164 0.2183 0.2485 REMARK 3 2 4.7807 - 3.7973 0.99 2754 137 0.2098 0.2391 REMARK 3 3 3.7973 - 3.3180 0.99 2700 138 0.2391 0.3236 REMARK 3 4 3.3180 - 3.0150 1.00 2696 144 0.2756 0.3250 REMARK 3 5 3.0150 - 2.7991 0.99 2663 151 0.2749 0.3759 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 2759 REMARK 3 ANGLE : 1.246 3776 REMARK 3 CHIRALITY : 0.047 414 REMARK 3 PLANARITY : 0.005 495 REMARK 3 DIHEDRAL : 14.249 965 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 63:154)) REMARK 3 ORIGIN FOR THE GROUP (A): -32.3638 -27.6028 -6.6527 REMARK 3 T TENSOR REMARK 3 T11: 1.0142 T22: 0.8523 REMARK 3 T33: 0.6675 T12: 0.1576 REMARK 3 T13: -0.1382 T23: 0.1044 REMARK 3 L TENSOR REMARK 3 L11: 1.1651 L22: 3.1548 REMARK 3 L33: 4.2663 L12: -0.4866 REMARK 3 L13: 1.3941 L23: -0.9708 REMARK 3 S TENSOR REMARK 3 S11: 0.0041 S12: 0.7125 S13: -0.0125 REMARK 3 S21: -0.6216 S22: -0.0051 S23: -0.0207 REMARK 3 S31: 0.8426 S32: 0.6072 S33: -0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 157:262) OR (RESSEQ 394:416)) REMARK 3 ORIGIN FOR THE GROUP (A): -31.1163 -3.3328 -35.2759 REMARK 3 T TENSOR REMARK 3 T11: 0.6084 T22: 0.8316 REMARK 3 T33: 0.7941 T12: -0.0720 REMARK 3 T13: -0.0174 T23: 0.3231 REMARK 3 L TENSOR REMARK 3 L11: 3.0977 L22: 3.2230 REMARK 3 L33: 2.7656 L12: -1.1631 REMARK 3 L13: 0.7261 L23: -1.5508 REMARK 3 S TENSOR REMARK 3 S11: 0.0418 S12: 0.0999 S13: -0.2384 REMARK 3 S21: 0.2679 S22: -0.7296 S23: -0.6717 REMARK 3 S31: 0.4859 S32: 1.3518 S33: -0.0451 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 263:393)) REMARK 3 ORIGIN FOR THE GROUP (A): -36.0885 19.1743 -47.1985 REMARK 3 T TENSOR REMARK 3 T11: 0.6936 T22: 0.6644 REMARK 3 T33: 0.7156 T12: -0.2935 REMARK 3 T13: 0.0016 T23: 0.1427 REMARK 3 L TENSOR REMARK 3 L11: 4.4413 L22: 4.6369 REMARK 3 L33: 3.3899 L12: 1.3174 REMARK 3 L13: -1.3252 L23: -0.9747 REMARK 3 S TENSOR REMARK 3 S11: 0.4047 S12: -0.1340 S13: 0.4728 REMARK 3 S21: 0.3690 S22: -0.6000 S23: -0.2655 REMARK 3 S31: -0.8319 S32: 0.8302 S33: -0.0450 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ZFQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000209172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.116 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14630 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.799 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 22.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05300 REMARK 200 FOR THE DATA SET : 53.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4Z7A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 85 MM SODIUM CITRATE, PH 5.6, 25.5% REMARK 280 PEG 4,000, 170 MM AMMONIUM ACETATE, AND 15% GLYCEROL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.5K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 128.92267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.46133 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 128.92267 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.46133 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 128.92267 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 64.46133 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 128.92267 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 64.46133 REMARK 290 REMARK 290 REMARK: NULL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 VAL A 2 REMARK 465 ILE A 3 REMARK 465 ARG A 4 REMARK 465 VAL A 5 REMARK 465 LEU A 6 REMARK 465 PHE A 7 REMARK 465 ARG A 8 REMARK 465 PRO A 9 REMARK 465 VAL A 10 REMARK 465 SER A 11 REMARK 465 LEU A 12 REMARK 465 ILE A 13 REMARK 465 PRO A 14 REMARK 465 VAL A 15 REMARK 465 ASN A 16 REMARK 465 ASN A 17 REMARK 465 SER A 18 REMARK 465 SER A 19 REMARK 465 THR A 20 REMARK 465 PRO A 21 REMARK 465 GLN A 22 REMARK 465 SER A 23 REMARK 465 GLN A 24 REMARK 465 GLY A 25 REMARK 465 PRO A 26 REMARK 465 ILE A 27 REMARK 465 SER A 28 REMARK 465 ARG A 29 REMARK 465 ARG A 30 REMARK 465 LEU A 31 REMARK 465 ALA A 32 REMARK 465 LEU A 33 REMARK 465 THR A 34 REMARK 465 ALA A 35 REMARK 465 LEU A 36 REMARK 465 GLY A 37 REMARK 465 PHE A 38 REMARK 465 GLY A 39 REMARK 465 VAL A 40 REMARK 465 LEU A 41 REMARK 465 ALA A 42 REMARK 465 PRO A 43 REMARK 465 ASN A 44 REMARK 465 VAL A 45 REMARK 465 LEU A 46 REMARK 465 VAL A 47 REMARK 465 ALA A 48 REMARK 465 CYS A 49 REMARK 465 ALA A 50 REMARK 465 GLY A 51 REMARK 465 LYS A 52 REMARK 465 VAL A 53 REMARK 465 THR A 54 REMARK 465 LYS A 55 REMARK 465 ALA A 320 REMARK 465 ALA A 321 REMARK 465 GLY A 322 REMARK 465 TYR A 323 REMARK 465 SER A 324 REMARK 465 HIS A 325 REMARK 465 ILE A 326 REMARK 465 GLY A 349 REMARK 465 ALA A 350 REMARK 465 GLN A 351 REMARK 465 GLY A 352 REMARK 465 ASN A 353 REMARK 465 SER A 354 REMARK 465 ASN A 355 REMARK 465 VAL A 356 REMARK 465 ALA A 417 REMARK 465 ALA A 418 REMARK 465 LYS A 419 REMARK 465 PRO A 420 REMARK 465 ALA A 421 REMARK 465 ALA A 422 REMARK 465 THR A 423 REMARK 465 GLN A 424 REMARK 465 ILE A 425 REMARK 465 PRO A 426 REMARK 465 VAL A 427 REMARK 465 THR A 428 REMARK 465 ALA A 429 REMARK 465 PRO A 430 REMARK 465 VAL A 431 REMARK 465 THR A 432 REMARK 465 PRO A 433 REMARK 465 SER A 434 REMARK 465 ASP A 435 REMARK 465 ALA A 436 REMARK 465 PRO A 437 REMARK 465 THR A 438 REMARK 465 PRO A 439 REMARK 465 SER A 440 REMARK 465 GLY A 441 REMARK 465 THR A 442 REMARK 465 PRO A 443 REMARK 465 THR A 444 REMARK 465 THR A 445 REMARK 465 THR A 446 REMARK 465 ASN A 447 REMARK 465 GLY A 448 REMARK 465 PRO A 449 REMARK 465 GLY A 450 REMARK 465 GLY A 451 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE A 314 CG CD1 CD2 CE1 CE2 CZ 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 PRO A 62 -150.56 -89.05 REMARK 500 ASP A 245 -143.32 61.95 REMARK 500 HIS A 272 28.85 48.28 REMARK 500 THR A 308 -70.38 -128.38 REMARK 500 ASN A 318 172.02 -49.41 REMARK 500 TRP A 330 52.25 34.69 REMARK 500 SER A 347 42.69 -152.51 REMARK 500 ASN A 358 -131.34 79.70 REMARK 500 CYS A 360 -163.45 -72.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 DWZ A 503 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DWZ A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Z7A RELATED DB: PDB REMARK 900 MYCOBACTERIUM TUBERCULOSIS (3,3)LD-TRANSPEPTIDASE TYPE 5 (LDTMT5; REMARK 900 MT50) APO-FORM DBREF 4ZFQ A 1 451 UNP P9WKV2 LDT5_MYCTO 1 451 SEQRES 1 A 451 MET VAL ILE ARG VAL LEU PHE ARG PRO VAL SER LEU ILE SEQRES 2 A 451 PRO VAL ASN ASN SER SER THR PRO GLN SER GLN GLY PRO SEQRES 3 A 451 ILE SER ARG ARG LEU ALA LEU THR ALA LEU GLY PHE GLY SEQRES 4 A 451 VAL LEU ALA PRO ASN VAL LEU VAL ALA CYS ALA GLY LYS SEQRES 5 A 451 VAL THR LYS LEU ALA GLU LYS ARG PRO PRO PRO ALA PRO SEQRES 6 A 451 ARG LEU THR PHE ARG PRO ALA ASP SER ALA ALA ASP VAL SEQRES 7 A 451 VAL PRO ILE ALA PRO ILE SER VAL GLU VAL GLY ASP GLY SEQRES 8 A 451 TRP PHE GLN ARG VAL ALA LEU THR ASN SER ALA GLY LYS SEQRES 9 A 451 VAL VAL ALA GLY ALA TYR SER ARG ASP ARG THR ILE TYR SEQRES 10 A 451 THR ILE THR GLU PRO LEU GLY TYR ASP THR THR TYR THR SEQRES 11 A 451 TRP SER GLY SER ALA VAL GLY HIS ASP GLY LYS ALA VAL SEQRES 12 A 451 PRO VAL ALA GLY LYS PHE THR THR VAL ALA PRO VAL LYS SEQRES 13 A 451 THR ILE ASN ALA GLY PHE GLN LEU ALA ASP GLY GLN THR SEQRES 14 A 451 VAL GLY ILE ALA ALA PRO VAL ILE ILE GLN PHE ASP SER SEQRES 15 A 451 PRO ILE SER ASP LYS ALA ALA VAL GLU ARG ALA LEU THR SEQRES 16 A 451 VAL THR THR ASP PRO PRO VAL GLU GLY GLY TRP ALA TRP SEQRES 17 A 451 LEU PRO ASP GLU ALA GLN GLY ALA ARG VAL HIS TRP ARG SEQRES 18 A 451 PRO ARG GLU TYR TYR PRO ALA GLY THR THR VAL ASP VAL SEQRES 19 A 451 ASP ALA LYS LEU TYR GLY LEU PRO PHE GLY ASP GLY ALA SEQRES 20 A 451 TYR GLY ALA GLN ASP MET SER LEU HIS PHE GLN ILE GLY SEQRES 21 A 451 ARG ARG GLN VAL VAL LYS ALA GLU VAL SER SER HIS ARG SEQRES 22 A 451 ILE GLN VAL VAL THR ASP ALA GLY VAL ILE MET ASP PHE SEQRES 23 A 451 PRO CYS SER TYR GLY GLU ALA ASP LEU ALA ARG ASN VAL SEQRES 24 A 451 THR ARG ASN GLY ILE HIS VAL VAL THR GLU LYS TYR SER SEQRES 25 A 451 ASP PHE TYR MET SER ASN PRO ALA ALA GLY TYR SER HIS SEQRES 26 A 451 ILE HIS GLU ARG TRP ALA VAL ARG ILE SER ASN ASN GLY SEQRES 27 A 451 GLU PHE ILE HIS ALA ASN PRO MET SER ALA GLY ALA GLN SEQRES 28 A 451 GLY ASN SER ASN VAL THR ASN GLY CYS ILE ASN LEU SER SEQRES 29 A 451 THR GLU ASN ALA GLU GLN TYR TYR ARG SER ALA VAL TYR SEQRES 30 A 451 GLY ASP PRO VAL GLU VAL THR GLY SER SER ILE GLN LEU SEQRES 31 A 451 SER TYR ALA ASP GLY ASP ILE TRP ASP TRP ALA VAL ASP SEQRES 32 A 451 TRP ASP THR TRP VAL SER MET SER ALA LEU PRO PRO PRO SEQRES 33 A 451 ALA ALA LYS PRO ALA ALA THR GLN ILE PRO VAL THR ALA SEQRES 34 A 451 PRO VAL THR PRO SER ASP ALA PRO THR PRO SER GLY THR SEQRES 35 A 451 PRO THR THR THR ASN GLY PRO GLY GLY HET PEG A 501 17 HET PEG A 502 17 HET DWZ A 503 28 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM DWZ (2S,3R,4S)-4-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN- HETNAM 2 DWZ 3-YL]SULFANYL}-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]- HETNAM 3 DWZ 3-METHYL-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID HETSYN DWZ MEROPENEM, BOUND FORM FORMUL 2 PEG 2(C4 H10 O3) FORMUL 4 DWZ C17 H27 N3 O5 S FORMUL 5 HOH *43(H2 O) HELIX 1 AA1 ASP A 186 ARG A 192 1 7 HELIX 2 AA2 SER A 364 ALA A 375 1 12 HELIX 3 AA3 SER A 391 GLY A 395 5 5 HELIX 4 AA4 TRP A 398 VAL A 402 5 5 HELIX 5 AA5 ASP A 403 MET A 410 1 8 SHEET 1 AA1 4 ARG A 66 ARG A 70 0 SHEET 2 AA1 4 SER A 85 GLY A 89 -1 O GLU A 87 N THR A 68 SHEET 3 AA1 4 ILE A 116 ILE A 119 -1 O TYR A 117 N VAL A 86 SHEET 4 AA1 4 GLY A 108 TYR A 110 -1 N ALA A 109 O THR A 118 SHEET 1 AA2 5 ALA A 75 VAL A 78 0 SHEET 2 AA2 5 GLY A 147 THR A 151 1 O THR A 150 N ALA A 75 SHEET 3 AA2 5 THR A 128 VAL A 136 -1 N TYR A 129 O PHE A 149 SHEET 4 AA2 5 TRP A 92 ASN A 100 -1 N THR A 99 O THR A 130 SHEET 5 AA2 5 VAL A 105 VAL A 106 -1 O VAL A 106 N LEU A 98 SHEET 1 AA3 4 ALA A 75 VAL A 78 0 SHEET 2 AA3 4 GLY A 147 THR A 151 1 O THR A 150 N ALA A 75 SHEET 3 AA3 4 THR A 128 VAL A 136 -1 N TYR A 129 O PHE A 149 SHEET 4 AA3 4 ALA A 142 PRO A 144 -1 O VAL A 143 N ALA A 135 SHEET 1 AA4 3 THR A 157 ILE A 158 0 SHEET 2 AA4 3 ALA A 247 GLY A 249 1 O TYR A 248 N ILE A 158 SHEET 3 AA4 3 PRO A 242 GLY A 244 -1 N GLY A 244 O ALA A 247 SHEET 1 AA5 4 THR A 169 VAL A 170 0 SHEET 2 AA5 4 MET A 253 ILE A 259 1 O GLN A 258 N VAL A 170 SHEET 3 AA5 4 THR A 231 ALA A 236 -1 N VAL A 232 O PHE A 257 SHEET 4 AA5 4 LEU A 194 ASP A 199 -1 N THR A 197 O ASP A 233 SHEET 1 AA6 3 VAL A 176 GLN A 179 0 SHEET 2 AA6 3 ARG A 217 PRO A 222 -1 O VAL A 218 N ILE A 178 SHEET 3 AA6 3 GLY A 204 TRP A 208 -1 N ALA A 207 O HIS A 219 SHEET 1 AA7 5 GLY A 281 PRO A 287 0 SHEET 2 AA7 5 ARG A 273 THR A 278 -1 N VAL A 276 O MET A 284 SHEET 3 AA7 5 GLN A 263 GLU A 268 -1 N LYS A 266 O GLN A 275 SHEET 4 AA7 5 PRO A 380 THR A 384 1 O GLU A 382 N ALA A 267 SHEET 5 AA7 5 GLY A 303 VAL A 306 -1 N HIS A 305 O VAL A 381 SHEET 1 AA8 4 LYS A 310 PHE A 314 0 SHEET 2 AA8 4 GLU A 328 ARG A 333 -1 O ALA A 331 N TYR A 311 SHEET 3 AA8 4 PHE A 340 ALA A 343 -1 O ALA A 343 N ARG A 329 SHEET 4 AA8 4 ILE A 361 LEU A 363 1 O LEU A 363 N HIS A 342 LINK SG CYS A 360 CAA DWZ A 503 1555 1555 1.75 CISPEP 1 ARG A 70 PRO A 71 0 1.48 CISPEP 2 ASP A 199 PRO A 200 0 -0.08 CISPEP 3 ASP A 396 ILE A 397 0 -7.24 SITE 1 AC1 3 VAL A 196 THR A 198 VAL A 202 SITE 1 AC2 2 LEU A 123 TYR A 239 SITE 1 AC3 9 ARG A 297 ASN A 318 GLU A 328 ASN A 337 SITE 2 AC3 9 GLY A 338 ASN A 358 GLY A 359 CYS A 360 SITE 3 AC3 9 HOH A 605 CRYST1 99.393 99.393 193.384 90.00 90.00 120.00 P 62 2 2 12 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 0.010061 0.005809 0.000000 0.00000 SCALE2 0.000000 0.011618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005171 0.00000