HEADER TRANSFERASE 20-NOV-17 6BOI TITLE CRYSTAL STRUCTURE OF LDTMT2 (56-408) WITH A PANIPENEM ADDUCT AT THE TITLE 2 ACTIVE SITE CYSTEINE-354 CAVEAT 6BOI E0Y A 501 HAS WRONG CHIRALITY AT ATOM CA E0Y A 501 HAS WRONG CAVEAT 2 6BOI CHIRALITY AT ATOM CB E0Y B 501 HAS WRONG CHIRALITY AT ATOM CAVEAT 3 6BOI CA E0Y B 501 HAS WRONG CHIRALITY AT ATOM CB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE CONSERVED LIPOPROTEIN LPPS; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 56-407; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25177 / SOURCE 3 H37RA); SOURCE 4 ORGANISM_TAXID: 419947; SOURCE 5 STRAIN: ATCC 25177 / H37RA; SOURCE 6 GENE: LPPS, MRA_2545; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS L, D-TRANSPEPTIDASE 2, CARBAPENEM, COMPLEX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.SAAVEDRA,M.A.BIANCHET REVDAT 2 04-OCT-23 6BOI 1 REMARK REVDAT 1 11-APR-18 6BOI 0 JRNL AUTH H.SAAVEDRA,M.A.BIANCHET JRNL TITL STRUCTURES AND MECHANISM OF INHIBITION OF MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS L,D-TRANSPEPTIDASE 2 BY PANIPENEM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.A.BIANCHET,Y.H.PAN,L.A.B.BASTA,H.SAAVEDRA,E.P.LLOYD, REMARK 1 AUTH 2 P.KUMAR,R.MATTOO,C.A.TOWNSEND,G.LAMICHHANE REMARK 1 TITL STRUCTURAL INSIGHT INTO THE INACTIVATION OF MYCOBACTERIUM REMARK 1 TITL 2 TUBERCULOSIS NON-CLASSICAL TRANSPEPTIDASE LDTMT2 BY BIAPENEM REMARK 1 TITL 3 AND TEBIPENEM. REMARK 1 REF BMC BIOCHEM. V. 18 8 2017 REMARK 1 REFN ESSN 1471-2091 REMARK 1 PMID 28545389 REMARK 1 DOI 10.1186/S12858-017-0082-4 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.A.BRAMMER BASTA,A.GHOSH,Y.PAN,J.JAKONCIC,E.P.LLOYD, REMARK 1 AUTH 2 C.A.TOWNSEND,G.LAMICHHANE,M.A.BIANCHET REMARK 1 TITL LOSS OF A FUNCTIONALLY AND STRUCTURALLY DISTINCT REMARK 1 TITL 2 LD-TRANSPEPTIDASE, LDTMT5, COMPROMISES CELL WALL INTEGRITY REMARK 1 TITL 3 IN MYCOBACTERIUM TUBERCULOSIS. REMARK 1 REF J. BIOL. CHEM. V. 290 25670 2015 REMARK 1 REFN ESSN 1083-351X REMARK 1 PMID 26304120 REMARK 1 DOI 10.1074/JBC.M115.660753 REMARK 1 REFERENCE 3 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. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 45570 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2297 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 51.1901 - 5.2947 0.99 2988 169 0.1659 0.1892 REMARK 3 2 5.2947 - 4.2032 1.00 2935 183 0.1308 0.1668 REMARK 3 3 4.2032 - 3.6721 1.00 2963 134 0.1424 0.1694 REMARK 3 4 3.6721 - 3.3364 1.00 2939 163 0.1509 0.1883 REMARK 3 5 3.3364 - 3.0973 1.00 2933 150 0.1602 0.2016 REMARK 3 6 3.0973 - 2.9147 1.00 2936 147 0.1634 0.2015 REMARK 3 7 2.9147 - 2.7687 1.00 2957 141 0.1761 0.2199 REMARK 3 8 2.7687 - 2.6482 0.99 2914 164 0.1781 0.2350 REMARK 3 9 2.6482 - 2.5463 1.00 2911 163 0.1867 0.2674 REMARK 3 10 2.5463 - 2.4584 0.99 2931 153 0.1863 0.2405 REMARK 3 11 2.4584 - 2.3815 0.99 2895 164 0.1919 0.2281 REMARK 3 12 2.3815 - 2.3135 0.99 2897 145 0.1872 0.2639 REMARK 3 13 2.3135 - 2.2526 0.85 2511 115 0.1940 0.2454 REMARK 3 14 2.2526 - 2.1976 0.72 2091 114 0.1969 0.2417 REMARK 3 15 2.1976 - 2.1476 0.64 1857 106 0.2011 0.2458 REMARK 3 16 2.1476 - 2.1019 0.55 1615 86 0.1952 0.2618 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.480 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 : 0.011 5599 REMARK 3 ANGLE : 1.134 7653 REMARK 3 CHIRALITY : 0.064 845 REMARK 3 PLANARITY : 0.006 997 REMARK 3 DIHEDRAL : 14.640 3217 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND ((RESSEQ 56:147)) REMARK 3 ORIGIN FOR THE GROUP (A): 11.4629 27.4422 0.3370 REMARK 3 T TENSOR REMARK 3 T11: 0.2444 T22: 0.3499 REMARK 3 T33: 0.2440 T12: 0.0505 REMARK 3 T13: 0.0179 T23: 0.0354 REMARK 3 L TENSOR REMARK 3 L11: 2.2245 L22: 7.5961 REMARK 3 L33: 4.4860 L12: 3.1116 REMARK 3 L13: 0.2310 L23: 3.0460 REMARK 3 S TENSOR REMARK 3 S11: -0.1672 S12: 0.0970 S13: -0.0880 REMARK 3 S21: -0.0173 S22: 0.1851 S23: -0.0231 REMARK 3 S31: 0.0508 S32: 0.1459 S33: 0.0151 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND ((RESSEQ 148:252)) REMARK 3 ORIGIN FOR THE GROUP (A): 9.1584 39.8645 30.9599 REMARK 3 T TENSOR REMARK 3 T11: 0.2095 T22: 0.1583 REMARK 3 T33: 0.2062 T12: 0.0313 REMARK 3 T13: -0.0272 T23: -0.0082 REMARK 3 L TENSOR REMARK 3 L11: 1.9507 L22: 1.4900 REMARK 3 L33: 4.8472 L12: 0.7079 REMARK 3 L13: -1.3481 L23: -0.5395 REMARK 3 S TENSOR REMARK 3 S11: -0.0016 S12: 0.0556 S13: -0.0537 REMARK 3 S21: -0.1019 S22: -0.0096 S23: -0.0252 REMARK 3 S31: -0.0331 S32: 0.2019 S33: 0.0157 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND ((RESSEQ 253:407)) REMARK 3 ORIGIN FOR THE GROUP (A): 13.9162 46.1047 54.4027 REMARK 3 T TENSOR REMARK 3 T11: 0.3103 T22: 0.2648 REMARK 3 T33: 0.2560 T12: -0.0614 REMARK 3 T13: 0.0015 T23: -0.0157 REMARK 3 L TENSOR REMARK 3 L11: 2.0571 L22: 2.0647 REMARK 3 L33: 1.6590 L12: 0.1916 REMARK 3 L13: 0.2679 L23: -0.4284 REMARK 3 S TENSOR REMARK 3 S11: 0.1453 S12: -0.3405 S13: 0.1515 REMARK 3 S21: 0.2568 S22: -0.2784 S23: -0.1804 REMARK 3 S31: -0.2411 S32: 0.1255 S33: 0.1310 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 56:147)) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5602 12.5367 35.6958 REMARK 3 T TENSOR REMARK 3 T11: 0.2283 T22: 0.2082 REMARK 3 T33: 0.2396 T12: -0.0402 REMARK 3 T13: 0.0298 T23: 0.0220 REMARK 3 L TENSOR REMARK 3 L11: 2.7156 L22: 6.3991 REMARK 3 L33: 3.3803 L12: -2.6371 REMARK 3 L13: -0.0974 L23: 2.8139 REMARK 3 S TENSOR REMARK 3 S11: -0.0213 S12: 0.0428 S13: 0.0597 REMARK 3 S21: 0.1697 S22: -0.0067 S23: -0.1707 REMARK 3 S31: 0.0490 S32: 0.0814 S33: 0.0377 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 148:252)) REMARK 3 ORIGIN FOR THE GROUP (A): 10.9874 0.2022 4.9382 REMARK 3 T TENSOR REMARK 3 T11: 0.2255 T22: 0.2843 REMARK 3 T33: 0.2846 T12: -0.0543 REMARK 3 T13: 0.0387 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 1.2567 L22: 1.5396 REMARK 3 L33: 5.1274 L12: -0.7305 REMARK 3 L13: 1.4116 L23: -0.7842 REMARK 3 S TENSOR REMARK 3 S11: -0.0596 S12: -0.0315 S13: -0.0654 REMARK 3 S21: -0.0066 S22: 0.1933 S23: 0.0607 REMARK 3 S31: -0.0868 S32: -0.0657 S33: -0.1248 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 253:407)) REMARK 3 ORIGIN FOR THE GROUP (A): 17.7827 -6.1324 -18.1700 REMARK 3 T TENSOR REMARK 3 T11: 0.3694 T22: 0.3611 REMARK 3 T33: 0.3036 T12: -0.0067 REMARK 3 T13: -0.0404 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 1.8485 L22: 3.2952 REMARK 3 L33: 1.2583 L12: -0.2380 REMARK 3 L13: 0.4649 L23: -1.1494 REMARK 3 S TENSOR REMARK 3 S11: 0.3328 S12: 0.1190 S13: -0.1615 REMARK 3 S21: -0.4247 S22: -0.3265 S23: -0.1334 REMARK 3 S31: 0.2098 S32: 0.1477 S33: 0.0071 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 6BOI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1000229901. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45570 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.102 REMARK 200 RESOLUTION RANGE LOW (A) : 51.175 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5D7H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% V/V PEG MONO-METHYL ESTER 5000 AND REMARK 280 180 MM AMMONIUM SULFATE, CRYSTALS WERE SOAKED IN 4 MM OF REMARK 280 PANIPENEM FOR 15 MINUTES, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 47.03000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 IN SAME ASYMMETRIC UNIT 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 HOH B 809 O HOH B 845 1.97 REMARK 500 O HOH A 726 O HOH B 804 1.97 REMARK 500 O HOH B 794 O HOH B 844 2.00 REMARK 500 ND1 HIS A 300 O HOH A 601 2.10 REMARK 500 O HOH B 673 O HOH B 809 2.10 REMARK 500 O HOH A 777 O HOH A 798 2.10 REMARK 500 O HOH B 798 O HOH B 813 2.12 REMARK 500 N ASN A 313 O2 SO4 A 510 2.17 REMARK 500 O HOH B 784 O HOH B 827 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ASP A 96 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES 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 ASN A 227 65.86 -105.55 REMARK 500 MET A 280 -165.56 -102.76 REMARK 500 HIS A 347 -58.15 -143.58 REMARK 500 ASN A 405 39.22 -148.66 REMARK 500 PHE B 215 151.90 -49.50 REMARK 500 ASN B 227 64.44 -101.03 REMARK 500 ASN B 269 44.94 39.86 REMARK 500 MET B 280 -169.69 -100.55 REMARK 500 HIS B 347 -56.75 -136.67 REMARK 500 ASN B 405 39.97 -147.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue E0Y 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 GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TUR RELATED DB: PDB REMARK 900 N-TERMINAL DOMAIN TRUNCATE LDTMT2 REMARK 900 RELATED ID: 5DC2 RELATED DB: PDB REMARK 900 BIAPENEM ADDUCT REMARK 900 RELATED ID: 5DCC RELATED DB: PDB REMARK 900 TEBIPENEM ADDUCT REMARK 900 RELATED ID: 5D7H RELATED DB: PDB REMARK 900 APO REMARK 900 RELATED ID: 3VYN RELATED DB: PDB REMARK 900 APO REMARK 900 RELATED ID: 4GSU RELATED DB: PDB REMARK 900 MEROPENEM ADDUCT REMARK 900 RELATED ID: 3TX4 RELATED DB: PDB REMARK 900 CYS354A MUTANT REMARK 900 RELATED ID: 3U1P RELATED DB: PDB REMARK 900 OXIDATED CYS354 REMARK 900 RELATED ID: 3U1Q RELATED DB: PDB REMARK 900 2-MERCAPTOETAHNOL ADDUCT DBREF 6BOI A 56 407 UNP A5U5L6 A5U5L6_MYCTA 56 407 DBREF 6BOI B 56 407 UNP A5U5L6 A5U5L6_MYCTA 56 407 SEQRES 1 A 352 ASP LEU LEU VAL PRO LYS LEU THR ALA SER VAL THR ASP SEQRES 2 A 352 GLY ALA VAL GLY VAL THR VAL ASP ALA PRO VAL SER VAL SEQRES 3 A 352 THR ALA ALA ASP GLY VAL LEU ALA ALA VAL THR MET VAL SEQRES 4 A 352 ASN ASP ASN GLY ARG PRO VAL ALA GLY ARG LEU SER PRO SEQRES 5 A 352 ASP GLY LEU ARG TRP SER THR THR GLU GLN LEU GLY TYR SEQRES 6 A 352 ASN ARG ARG TYR THR LEU ASN ALA THR ALA LEU GLY LEU SEQRES 7 A 352 GLY GLY ALA ALA THR ARG GLN LEU THR PHE GLN THR SER SEQRES 8 A 352 SER PRO ALA HIS LEU THR MET PRO TYR VAL MET PRO GLY SEQRES 9 A 352 ASP GLY GLU VAL VAL GLY VAL GLY GLU PRO VAL ALA ILE SEQRES 10 A 352 ARG PHE ASP GLU ASN ILE ALA ASP ARG GLY ALA ALA GLU SEQRES 11 A 352 LYS ALA ILE LYS ILE THR THR ASN PRO PRO VAL GLU GLY SEQRES 12 A 352 ALA PHE TYR TRP LEU ASN ASN ARG GLU VAL ARG TRP ARG SEQRES 13 A 352 PRO GLU HIS PHE TRP LYS PRO GLY THR ALA VAL ASP VAL SEQRES 14 A 352 ALA VAL ASN THR TYR GLY VAL ASP LEU GLY GLU GLY MET SEQRES 15 A 352 PHE GLY GLU ASP ASN VAL GLN THR HIS PHE THR ILE GLY SEQRES 16 A 352 ASP GLU VAL ILE ALA THR ALA ASP ASP ASN THR LYS ILE SEQRES 17 A 352 LEU THR VAL ARG VAL ASN GLY GLU VAL VAL LYS SER MET SEQRES 18 A 352 PRO THR SER MET GLY LYS ASP SER THR PRO THR ALA ASN SEQRES 19 A 352 GLY ILE TYR ILE VAL GLY SER ARG TYR LYS HIS ILE ILE SEQRES 20 A 352 MET ASP SER SER THR TYR GLY VAL PRO VAL ASN SER PRO SEQRES 21 A 352 ASN GLY TYR ARG THR ASP VAL ASP TRP ALA THR GLN ILE SEQRES 22 A 352 SER TYR SER GLY VAL PHE VAL HIS SER ALA PRO TRP SER SEQRES 23 A 352 VAL GLY ALA GLN GLY HIS THR ASN THR SER HIS GLY CYS SEQRES 24 A 352 LEU ASN VAL SER PRO SER ASN ALA GLN TRP PHE TYR ASP SEQRES 25 A 352 HIS VAL LYS ARG GLY ASP ILE VAL GLU VAL VAL ASN THR SEQRES 26 A 352 VAL GLY GLY THR LEU PRO GLY ILE ASP GLY LEU GLY ASP SEQRES 27 A 352 TRP ASN ILE PRO TRP ASP GLN TRP ARG ALA GLY ASN ALA SEQRES 28 A 352 LYS SEQRES 1 B 352 ASP LEU LEU VAL PRO LYS LEU THR ALA SER VAL THR ASP SEQRES 2 B 352 GLY ALA VAL GLY VAL THR VAL ASP ALA PRO VAL SER VAL SEQRES 3 B 352 THR ALA ALA ASP GLY VAL LEU ALA ALA VAL THR MET VAL SEQRES 4 B 352 ASN ASP ASN GLY ARG PRO VAL ALA GLY ARG LEU SER PRO SEQRES 5 B 352 ASP GLY LEU ARG TRP SER THR THR GLU GLN LEU GLY TYR SEQRES 6 B 352 ASN ARG ARG TYR THR LEU ASN ALA THR ALA LEU GLY LEU SEQRES 7 B 352 GLY GLY ALA ALA THR ARG GLN LEU THR PHE GLN THR SER SEQRES 8 B 352 SER PRO ALA HIS LEU THR MET PRO TYR VAL MET PRO GLY SEQRES 9 B 352 ASP GLY GLU VAL VAL GLY VAL GLY GLU PRO VAL ALA ILE SEQRES 10 B 352 ARG PHE ASP GLU ASN ILE ALA ASP ARG GLY ALA ALA GLU SEQRES 11 B 352 LYS ALA ILE LYS ILE THR THR ASN PRO PRO VAL GLU GLY SEQRES 12 B 352 ALA PHE TYR TRP LEU ASN ASN ARG GLU VAL ARG TRP ARG SEQRES 13 B 352 PRO GLU HIS PHE TRP LYS PRO GLY THR ALA VAL ASP VAL SEQRES 14 B 352 ALA VAL ASN THR TYR GLY VAL ASP LEU GLY GLU GLY MET SEQRES 15 B 352 PHE GLY GLU ASP ASN VAL GLN THR HIS PHE THR ILE GLY SEQRES 16 B 352 ASP GLU VAL ILE ALA THR ALA ASP ASP ASN THR LYS ILE SEQRES 17 B 352 LEU THR VAL ARG VAL ASN GLY GLU VAL VAL LYS SER MET SEQRES 18 B 352 PRO THR SER MET GLY LYS ASP SER THR PRO THR ALA ASN SEQRES 19 B 352 GLY ILE TYR ILE VAL GLY SER ARG TYR LYS HIS ILE ILE SEQRES 20 B 352 MET ASP SER SER THR TYR GLY VAL PRO VAL ASN SER PRO SEQRES 21 B 352 ASN GLY TYR ARG THR ASP VAL ASP TRP ALA THR GLN ILE SEQRES 22 B 352 SER TYR SER GLY VAL PHE VAL HIS SER ALA PRO TRP SER SEQRES 23 B 352 VAL GLY ALA GLN GLY HIS THR ASN THR SER HIS GLY CYS SEQRES 24 B 352 LEU ASN VAL SER PRO SER ASN ALA GLN TRP PHE TYR ASP SEQRES 25 B 352 HIS VAL LYS ARG GLY ASP ILE VAL GLU VAL VAL ASN THR SEQRES 26 B 352 VAL GLY GLY THR LEU PRO GLY ILE ASP GLY LEU GLY ASP SEQRES 27 B 352 TRP ASN ILE PRO TRP ASP GLN TRP ARG ALA GLY ASN ALA SEQRES 28 B 352 LYS HET E0Y A 501 23 HET PEG A 502 17 HET GOL A 503 14 HET GOL A 504 14 HET GOL A 505 14 HET GOL A 506 14 HET GOL A 507 14 HET SO4 A 508 5 HET SO4 A 509 5 HET SO4 A 510 5 HET SO4 A 511 5 HET E0Y B 501 23 HET PEG B 502 17 HET PEG B 503 17 HET GOL B 504 14 HET GOL B 505 14 HET SO4 B 506 5 HETNAM E0Y (3S,5R)-5-[(2R,3R)-1,3-DIHYDROXYBUTAN-2-YL]-3-({(3R)-1- HETNAM 2 E0Y [(1E)-ETHANIMIDOYL]PYRROLIDIN-3-YL}SULFANYL)-L-PROLINE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 E0Y 2(C15 H27 N3 O4 S) FORMUL 4 PEG 3(C4 H10 O3) FORMUL 5 GOL 7(C3 H8 O3) FORMUL 10 SO4 5(O4 S 2-) FORMUL 20 HOH *488(H2 O) HELIX 1 AA1 ASP A 180 ALA A 187 1 8 HELIX 2 AA2 SER A 306 GLY A 309 5 4 HELIX 3 AA3 PRO A 339 GLN A 345 5 7 HELIX 4 AA4 SER A 358 VAL A 369 1 12 HELIX 5 AA5 GLY A 392 ILE A 396 5 5 HELIX 6 AA6 PRO A 397 GLY A 404 1 8 HELIX 7 AA7 ASP B 180 ALA B 187 1 8 HELIX 8 AA8 SER B 306 GLY B 309 5 4 HELIX 9 AA9 PRO B 339 VAL B 342 5 4 HELIX 10 AB1 SER B 358 VAL B 369 1 12 HELIX 11 AB2 GLY B 392 ILE B 396 5 5 HELIX 12 AB3 PRO B 397 GLY B 404 1 8 SHEET 1 AA1 4 LYS A 61 ALA A 64 0 SHEET 2 AA1 4 SER A 80 ALA A 84 -1 O THR A 82 N THR A 63 SHEET 3 AA1 4 ARG A 111 THR A 114 -1 O TRP A 112 N VAL A 81 SHEET 4 AA1 4 GLY A 103 LEU A 105 -1 N ARG A 104 O SER A 113 SHEET 1 AA2 3 VAL A 87 VAL A 94 0 SHEET 2 AA2 3 ARG A 123 GLY A 132 -1 O THR A 129 N ALA A 89 SHEET 3 AA2 3 GLY A 135 GLN A 144 -1 O LEU A 141 N LEU A 126 SHEET 1 AA3 2 HIS A 150 THR A 152 0 SHEET 2 AA3 2 MET A 237 GLY A 239 1 O PHE A 238 N HIS A 150 SHEET 1 AA4 4 PRO A 154 MET A 157 0 SHEET 2 AA4 4 VAL A 170 PHE A 174 -1 O ALA A 171 N MET A 157 SHEET 3 AA4 4 GLU A 207 PRO A 212 -1 O TRP A 210 N VAL A 170 SHEET 4 AA4 4 GLY A 198 TRP A 202 -1 N TYR A 201 O ARG A 209 SHEET 1 AA5 4 VAL A 163 VAL A 164 0 SHEET 2 AA5 4 VAL A 243 ILE A 249 1 O THR A 248 N VAL A 164 SHEET 3 AA5 4 ALA A 221 VAL A 226 -1 N VAL A 224 O THR A 245 SHEET 4 AA5 4 ILE A 188 ASN A 193 -1 N ASN A 193 O ALA A 221 SHEET 1 AA6 5 GLU A 271 PRO A 277 0 SHEET 2 AA6 5 ILE A 263 VAL A 268 -1 N VAL A 266 O LYS A 274 SHEET 3 AA6 5 VAL A 253 ASP A 258 -1 N THR A 256 O THR A 265 SHEET 4 AA6 5 ILE A 374 VAL A 378 1 O GLU A 376 N ALA A 257 SHEET 5 AA6 5 GLY A 290 ILE A 293 -1 N TYR A 292 O VAL A 375 SHEET 1 AA7 4 ARG A 297 ASP A 304 0 SHEET 2 AA7 4 ARG A 319 GLN A 327 -1 O ALA A 325 N TYR A 298 SHEET 3 AA7 4 PHE A 334 SER A 337 -1 O VAL A 335 N THR A 326 SHEET 4 AA7 4 LEU A 355 VAL A 357 1 O LEU A 355 N PHE A 334 SHEET 1 AA8 4 LYS B 61 ALA B 64 0 SHEET 2 AA8 4 SER B 80 ALA B 84 -1 O THR B 82 N THR B 63 SHEET 3 AA8 4 ARG B 111 THR B 114 -1 O TRP B 112 N VAL B 81 SHEET 4 AA8 4 GLY B 103 LEU B 105 -1 N ARG B 104 O SER B 113 SHEET 1 AA9 3 VAL B 87 VAL B 94 0 SHEET 2 AA9 3 ARG B 123 GLY B 132 -1 O THR B 129 N ALA B 89 SHEET 3 AA9 3 GLY B 135 GLN B 144 -1 O LEU B 141 N LEU B 126 SHEET 1 AB1 2 HIS B 150 THR B 152 0 SHEET 2 AB1 2 MET B 237 GLY B 239 1 O PHE B 238 N HIS B 150 SHEET 1 AB2 4 PRO B 154 MET B 157 0 SHEET 2 AB2 4 VAL B 170 PHE B 174 -1 O ARG B 173 N TYR B 155 SHEET 3 AB2 4 GLU B 207 PRO B 212 -1 O VAL B 208 N ILE B 172 SHEET 4 AB2 4 GLY B 198 TRP B 202 -1 N TYR B 201 O ARG B 209 SHEET 1 AB3 4 VAL B 163 VAL B 164 0 SHEET 2 AB3 4 VAL B 243 ILE B 249 1 O THR B 248 N VAL B 164 SHEET 3 AB3 4 ALA B 221 VAL B 226 -1 N VAL B 226 O VAL B 243 SHEET 4 AB3 4 ILE B 188 ASN B 193 -1 N ASN B 193 O ALA B 221 SHEET 1 AB4 5 GLU B 271 PRO B 277 0 SHEET 2 AB4 5 ILE B 263 VAL B 268 -1 N LEU B 264 O MET B 276 SHEET 3 AB4 5 VAL B 253 ASP B 258 -1 N THR B 256 O THR B 265 SHEET 4 AB4 5 ILE B 374 VAL B 378 1 O ILE B 374 N ALA B 255 SHEET 5 AB4 5 GLY B 290 ILE B 293 -1 N TYR B 292 O VAL B 375 SHEET 1 AB5 4 ARG B 297 ASP B 304 0 SHEET 2 AB5 4 ARG B 319 GLN B 327 -1 O THR B 320 N MET B 303 SHEET 3 AB5 4 PHE B 334 SER B 337 -1 O VAL B 335 N THR B 326 SHEET 4 AB5 4 LEU B 355 VAL B 357 1 O LEU B 355 N PHE B 334 LINK SG CYS A 354 C7 E0Y A 501 1555 1555 1.71 LINK SG CYS B 354 C7 E0Y B 501 1555 1555 1.86 CISPEP 1 MET A 157 PRO A 158 0 -0.05 CISPEP 2 ASN A 193 PRO A 194 0 5.79 CISPEP 3 MET B 157 PRO B 158 0 0.62 CISPEP 4 ASN B 193 PRO B 194 0 2.20 SITE 1 AC1 11 MET A 303 TYR A 318 THR A 320 GLY A 332 SITE 2 AC1 11 HIS A 336 TRP A 340 SER A 351 HIS A 352 SITE 3 AC1 11 GLY A 353 CYS A 354 ASN A 356 SITE 1 AC2 6 GLY A 86 GLY A 132 LEU A 133 PRO B 194 SITE 2 AC2 6 GLY B 219 HOH B 740 SITE 1 AC3 6 VAL A 75 ALA A 77 PRO A 78 GLN A 117 SITE 2 AC3 6 LEU A 118 HOH A 744 SITE 1 AC4 4 VAL A 91 TRP A 112 HOH A 719 ASP B 160 SITE 1 AC5 3 GLU A 213 HIS A 214 PHE A 215 SITE 1 AC6 2 ASP A 251 HIS A 368 SITE 1 AC7 3 TYR A 330 SER A 331 ASP A 389 SITE 1 AC8 3 THR A 92 ASN A 127 HOH A 657 SITE 1 AC9 5 THR A 63 SER A 65 SER A 80 THR A 82 SITE 2 AC9 5 ARG A 111 SITE 1 AD1 4 PRO A 311 VAL A 312 ASN A 313 HOH A 694 SITE 1 AD2 3 GLU A 162 ARG A 371 HOH A 730 SITE 1 AD3 4 SER B 306 PRO B 311 VAL B 312 ASN B 313 SITE 1 AD4 2 HOH B 635 HOH B 718 SITE 1 AD5 6 PRO B 386 GLY B 387 ILE B 388 ASN B 395 SITE 2 AD5 6 HOH B 603 HOH B 802 SITE 1 AD6 5 ILE B 188 LYS B 189 ILE B 190 GLY B 198 SITE 2 AD6 5 TRP B 210 SITE 1 AD7 5 ARG B 297 ARG B 371 HOH B 646 HOH B 668 SITE 2 AD7 5 HOH B 708 CRYST1 61.060 94.060 75.400 90.00 92.70 90.00 P 1 21 1 4 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 0.016377 0.000000 0.000772 0.00000 SCALE2 0.000000 0.010632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013277 0.00000