HEADER TRANSFERASE 13-JAN-20 6LQB TITLE A THIRD INTERMEDIATE STATE OF L,D-TRANSPEPTIDASE LDTMT2-ERTAPENEM TITLE 2 ADDUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: L,D-TRANSPEPTIDASE 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LDT 2,LDT(MT2); COMPND 5 EC: 2.3.2.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 STRAIN: ATCC 25618 / H37RV; SOURCE 6 GENE: LDTB, LPPS, RV2518C, RVBD_2518C, P425_02624; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS YKUD DOMAIN, L, D-TRANSPEPTIDASE, BETA-LACTAM BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.F.LI,Y.L.QIN REVDAT 3 29-NOV-23 6LQB 1 REMARK REVDAT 2 28-JUL-21 6LQB 1 JRNL REVDAT 1 13-JAN-21 6LQB 0 JRNL AUTH X.Y.WANG,Y.L.QIN,Q.HAN,X.E.GU,Z.YAN,K.FU,D.F.LI,K.DENG JRNL TITL A NEW STATE I-PLUS OBSERVED FOR THE L,D-TRANSPEPTIDASE JRNL TITL 2 LDTMT2-ERTAPENEM ADDUCT JRNL REF PROG.BIOCHEM.BIOPHYS. V. 47 989 2020 JRNL REFN ISSN 1000-3282 JRNL DOI 10.16476/J.PIBB.2020.0079 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 57794 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.470 REMARK 3 FREE R VALUE TEST SET COUNT : 2003 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 44.9690 - 4.0963 1.00 4229 148 0.1823 0.1894 REMARK 3 2 4.0963 - 3.2516 1.00 4068 144 0.1643 0.1899 REMARK 3 3 3.2516 - 2.8407 1.00 4026 141 0.1703 0.1928 REMARK 3 4 2.8407 - 2.5810 1.00 4000 146 0.1809 0.2305 REMARK 3 5 2.5810 - 2.3960 1.00 3988 143 0.1784 0.2131 REMARK 3 6 2.3960 - 2.2547 1.00 3959 148 0.1807 0.2080 REMARK 3 7 2.2547 - 2.1418 1.00 3964 136 0.1742 0.2012 REMARK 3 8 2.1418 - 2.0486 1.00 3964 139 0.1731 0.2080 REMARK 3 9 2.0486 - 1.9697 1.00 3943 156 0.1768 0.2103 REMARK 3 10 1.9697 - 1.9018 1.00 3951 129 0.1800 0.2410 REMARK 3 11 1.9018 - 1.8423 1.00 3923 142 0.1911 0.2338 REMARK 3 12 1.8423 - 1.7896 1.00 3923 144 0.2140 0.2731 REMARK 3 13 1.7896 - 1.7425 1.00 3946 144 0.2404 0.2503 REMARK 3 14 1.7425 - 1.7000 1.00 3907 143 0.2613 0.3252 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.17 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 141 THROUGH 289 ) REMARK 3 ORIGIN FOR THE GROUP (A): -39.8971 -13.1262 -13.8860 REMARK 3 T TENSOR REMARK 3 T11: 0.1578 T22: 0.1894 REMARK 3 T33: 0.1434 T12: -0.0168 REMARK 3 T13: 0.0065 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.6417 L22: 1.8004 REMARK 3 L33: 0.5020 L12: -0.2141 REMARK 3 L13: 0.0767 L23: -0.1128 REMARK 3 S TENSOR REMARK 3 S11: 0.0346 S12: -0.0647 S13: -0.0838 REMARK 3 S21: 0.1049 S22: -0.0532 S23: 0.0275 REMARK 3 S31: 0.0603 S32: 0.0095 S33: 0.0194 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 290 THROUGH 323 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.7716 6.3708 -0.2607 REMARK 3 T TENSOR REMARK 3 T11: 0.2966 T22: 0.3352 REMARK 3 T33: 0.3309 T12: 0.0507 REMARK 3 T13: -0.0675 T23: -0.1466 REMARK 3 L TENSOR REMARK 3 L11: 0.0596 L22: 1.7090 REMARK 3 L33: 1.4864 L12: -0.4871 REMARK 3 L13: -0.3427 L23: 0.9086 REMARK 3 S TENSOR REMARK 3 S11: -0.0195 S12: -0.2631 S13: 0.2848 REMARK 3 S21: 0.5943 S22: 0.4622 S23: -0.6161 REMARK 3 S31: 0.3037 S32: 0.4632 S33: -0.2603 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 324 THROUGH 407 ) REMARK 3 ORIGIN FOR THE GROUP (A): -40.1213 3.4362 -13.8118 REMARK 3 T TENSOR REMARK 3 T11: 0.1508 T22: 0.1619 REMARK 3 T33: 0.1635 T12: -0.0171 REMARK 3 T13: 0.0036 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 0.6601 L22: 1.3012 REMARK 3 L33: 0.7361 L12: -0.4527 REMARK 3 L13: -0.0668 L23: 0.3066 REMARK 3 S TENSOR REMARK 3 S11: 0.0150 S12: -0.0320 S13: 0.0278 REMARK 3 S21: 0.0656 S22: -0.0158 S23: -0.0640 REMARK 3 S31: -0.0271 S32: -0.0153 S33: 0.0009 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 142 THROUGH 164 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.2039 -24.4570 -6.0681 REMARK 3 T TENSOR REMARK 3 T11: 0.5406 T22: 0.3814 REMARK 3 T33: 0.4046 T12: -0.0357 REMARK 3 T13: -0.0940 T23: 0.1063 REMARK 3 L TENSOR REMARK 3 L11: 1.1540 L22: 1.9096 REMARK 3 L33: 1.2748 L12: 0.0153 REMARK 3 L13: 0.1979 L23: -0.6643 REMARK 3 S TENSOR REMARK 3 S11: 0.3156 S12: -0.1671 S13: -0.7369 REMARK 3 S21: 0.3690 S22: -0.1506 S23: 0.1736 REMARK 3 S31: 0.5668 S32: 0.2112 S33: -0.1456 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 165 THROUGH 212 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.6804 -17.7228 -15.9420 REMARK 3 T TENSOR REMARK 3 T11: 0.3362 T22: 0.2128 REMARK 3 T33: 0.1938 T12: 0.1015 REMARK 3 T13: -0.0300 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.6666 L22: 1.1774 REMARK 3 L33: 1.2889 L12: -0.0373 REMARK 3 L13: -0.4983 L23: -0.4836 REMARK 3 S TENSOR REMARK 3 S11: 0.2619 S12: 0.1310 S13: -0.2401 REMARK 3 S21: -0.3151 S22: -0.2202 S23: 0.0764 REMARK 3 S31: 0.7277 S32: 0.3778 S33: -0.0169 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 213 THROUGH 226 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.0354 -12.4907 -22.5317 REMARK 3 T TENSOR REMARK 3 T11: 0.3402 T22: 0.1902 REMARK 3 T33: 0.1959 T12: -0.0160 REMARK 3 T13: -0.0433 T23: -0.0105 REMARK 3 L TENSOR REMARK 3 L11: 2.2234 L22: 2.5641 REMARK 3 L33: 1.4415 L12: -0.9511 REMARK 3 L13: 0.6185 L23: -0.9606 REMARK 3 S TENSOR REMARK 3 S11: 0.3211 S12: 0.1872 S13: -0.2665 REMARK 3 S21: -0.2545 S22: -0.0212 S23: 0.3480 REMARK 3 S31: 0.4301 S32: -0.0499 S33: -0.2855 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 227 THROUGH 249 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.1760 -26.0490 -9.9059 REMARK 3 T TENSOR REMARK 3 T11: 0.8929 T22: 0.2291 REMARK 3 T33: 0.4271 T12: 0.0571 REMARK 3 T13: -0.2180 T23: 0.0623 REMARK 3 L TENSOR REMARK 3 L11: 0.4856 L22: 2.2933 REMARK 3 L33: 1.0538 L12: -0.7717 REMARK 3 L13: 0.3915 L23: -1.4098 REMARK 3 S TENSOR REMARK 3 S11: 0.2835 S12: -0.4329 S13: -0.5770 REMARK 3 S21: 0.1121 S22: 0.2580 S23: 0.2627 REMARK 3 S31: 1.3191 S32: -0.3501 S33: -0.2640 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 250 THROUGH 289 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.3420 10.8930 -19.0528 REMARK 3 T TENSOR REMARK 3 T11: 0.1553 T22: 0.1719 REMARK 3 T33: 0.1612 T12: -0.0110 REMARK 3 T13: -0.0042 T23: 0.0088 REMARK 3 L TENSOR REMARK 3 L11: 0.7350 L22: 1.1998 REMARK 3 L33: 0.9853 L12: -0.3833 REMARK 3 L13: -0.1902 L23: -0.0456 REMARK 3 S TENSOR REMARK 3 S11: -0.0428 S12: 0.0906 S13: 0.0487 REMARK 3 S21: -0.0499 S22: 0.0303 S23: 0.0783 REMARK 3 S31: -0.1119 S32: 0.0507 S33: -0.0112 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 290 THROUGH 308 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.8047 4.0533 -3.7117 REMARK 3 T TENSOR REMARK 3 T11: 0.2122 T22: 0.1822 REMARK 3 T33: 0.1774 T12: 0.0032 REMARK 3 T13: 0.0147 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 0.5510 L22: 0.7823 REMARK 3 L33: 1.9469 L12: 0.0966 REMARK 3 L13: -0.0451 L23: 0.6825 REMARK 3 S TENSOR REMARK 3 S11: 0.0245 S12: -0.1503 S13: 0.0703 REMARK 3 S21: 0.2318 S22: 0.0046 S23: -0.0826 REMARK 3 S31: 0.1261 S32: 0.0120 S33: -0.0032 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 309 THROUGH 323 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.1796 12.9755 4.2091 REMARK 3 T TENSOR REMARK 3 T11: 0.3646 T22: 0.3064 REMARK 3 T33: 0.4174 T12: -0.0096 REMARK 3 T13: -0.0316 T23: -0.0619 REMARK 3 L TENSOR REMARK 3 L11: 2.6533 L22: 0.7218 REMARK 3 L33: 2.1503 L12: -1.0004 REMARK 3 L13: 1.4981 L23: 0.0628 REMARK 3 S TENSOR REMARK 3 S11: 0.0269 S12: -0.0498 S13: 0.2132 REMARK 3 S21: 0.2238 S22: 0.0237 S23: -0.5373 REMARK 3 S31: -0.1678 S32: 0.2249 S33: -0.0115 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 324 THROUGH 405 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.5486 5.1258 -13.4666 REMARK 3 T TENSOR REMARK 3 T11: 0.1496 T22: 0.1645 REMARK 3 T33: 0.1331 T12: 0.0223 REMARK 3 T13: -0.0002 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 0.8628 L22: 1.1708 REMARK 3 L33: 1.5018 L12: 0.2408 REMARK 3 L13: -0.0772 L23: 0.1852 REMARK 3 S TENSOR REMARK 3 S11: -0.0482 S12: -0.0290 S13: -0.0330 REMARK 3 S21: 0.0508 S22: 0.0349 S23: -0.0150 REMARK 3 S31: 0.0445 S32: 0.0959 S33: 0.0136 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 142 THROUGH 155 OR REMARK 3 RESID 157 THROUGH 405)) REMARK 3 SELECTION : (CHAIN B AND (RESID 142 THROUGH 155 OR REMARK 3 RESID 157 THROUGH 405)) REMARK 3 ATOM PAIRS NUMBER : 1586 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6LQB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1300014006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9777 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57876 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 44.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 13.30 REMARK 200 R MERGE FOR SHELL (I) : 0.98000 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: PHASER REMARK 200 STARTING MODEL: 3VYP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM TRIS-HCL PH 8.0, 150 MM NACL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 34.09050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.90150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.60350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.90150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.09050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.60350 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 GLN A 140 REMARK 465 ALA A 408 REMARK 465 GLN B 140 REMARK 465 LEU B 141 REMARK 465 ALA B 406 REMARK 465 LYS B 407 REMARK 465 ALA B 408 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 PRO A 311 OG SER A 314 2.04 REMARK 500 O HOH A 640 O HOH A 779 2.06 REMARK 500 NZ LYS A 217 O HOH A 601 2.14 REMARK 500 OG SER A 305 O VAL A 310 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 723 O HOH B 616 4445 1.91 REMARK 500 O HOH A 670 O HOH B 730 4445 2.13 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 HIS A 150 28.37 -142.93 REMARK 500 ASN A 227 59.95 -98.98 REMARK 500 MET A 280 -166.19 -102.35 REMARK 500 ASN A 313 36.24 -90.72 REMARK 500 HIS A 347 -54.79 -134.85 REMARK 500 ASN A 405 30.67 -140.95 REMARK 500 ALA A 406 -73.03 -86.75 REMARK 500 HIS B 150 142.88 85.93 REMARK 500 ASN B 204 -168.54 -161.25 REMARK 500 MET B 280 -166.78 -103.02 REMARK 500 ASN B 313 41.18 -89.63 REMARK 500 HIS B 347 -51.05 -136.66 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 2RG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL 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 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACY B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide 2RG B 501 and CYS B REMARK 800 354 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VYP RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH DIFFERENT LIGAND REMARK 900 RELATED ID: 6IYV RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH THE SAME LIGAND IN DIFFERENT CONFORMATION DBREF 6LQB A 140 408 UNP I6Y9J2 LDT2_MYCTU 140 408 DBREF 6LQB B 140 408 UNP I6Y9J2 LDT2_MYCTU 140 408 SEQRES 1 A 269 GLN LEU THR PHE GLN THR SER SER PRO ALA HIS LEU THR SEQRES 2 A 269 MET PRO TYR VAL MET PRO GLY ASP GLY GLU VAL VAL GLY SEQRES 3 A 269 VAL GLY GLU PRO VAL ALA ILE ARG PHE ASP GLU ASN ILE SEQRES 4 A 269 ALA ASP ARG GLY ALA ALA GLU LYS ALA ILE LYS ILE THR SEQRES 5 A 269 THR ASN PRO PRO VAL GLU GLY ALA PHE TYR TRP LEU ASN SEQRES 6 A 269 ASN ARG GLU VAL ARG TRP ARG PRO GLU HIS PHE TRP LYS SEQRES 7 A 269 PRO GLY THR ALA VAL ASP VAL ALA VAL ASN THR TYR GLY SEQRES 8 A 269 VAL ASP LEU GLY GLU GLY MET PHE GLY GLU ASP ASN VAL SEQRES 9 A 269 GLN THR HIS PHE THR ILE GLY ASP GLU VAL ILE ALA THR SEQRES 10 A 269 ALA ASP ASP ASN THR LYS ILE LEU THR VAL ARG VAL ASN SEQRES 11 A 269 GLY GLU VAL VAL LYS SER MET PRO THR SER MET GLY LYS SEQRES 12 A 269 ASP SER THR PRO THR ALA ASN GLY ILE TYR ILE VAL GLY SEQRES 13 A 269 SER ARG TYR LYS HIS ILE ILE MET ASP SER SER THR TYR SEQRES 14 A 269 GLY VAL PRO VAL ASN SER PRO ASN GLY TYR ARG THR ASP SEQRES 15 A 269 VAL ASP TRP ALA THR GLN ILE SER TYR SER GLY VAL PHE SEQRES 16 A 269 VAL HIS SER ALA PRO TRP SER VAL GLY ALA GLN GLY HIS SEQRES 17 A 269 THR ASN THR SER HIS GLY CYS LEU ASN VAL SER PRO SER SEQRES 18 A 269 ASN ALA GLN TRP PHE TYR ASP HIS VAL LYS ARG GLY ASP SEQRES 19 A 269 ILE VAL GLU VAL VAL ASN THR VAL GLY GLY THR LEU PRO SEQRES 20 A 269 GLY ILE ASP GLY LEU GLY ASP TRP ASN ILE PRO TRP ASP SEQRES 21 A 269 GLN TRP ARG ALA GLY ASN ALA LYS ALA SEQRES 1 B 269 GLN LEU THR PHE GLN THR SER SER PRO ALA HIS LEU THR SEQRES 2 B 269 MET PRO TYR VAL MET PRO GLY ASP GLY GLU VAL VAL GLY SEQRES 3 B 269 VAL GLY GLU PRO VAL ALA ILE ARG PHE ASP GLU ASN ILE SEQRES 4 B 269 ALA ASP ARG GLY ALA ALA GLU LYS ALA ILE LYS ILE THR SEQRES 5 B 269 THR ASN PRO PRO VAL GLU GLY ALA PHE TYR TRP LEU ASN SEQRES 6 B 269 ASN ARG GLU VAL ARG TRP ARG PRO GLU HIS PHE TRP LYS SEQRES 7 B 269 PRO GLY THR ALA VAL ASP VAL ALA VAL ASN THR TYR GLY SEQRES 8 B 269 VAL ASP LEU GLY GLU GLY MET PHE GLY GLU ASP ASN VAL SEQRES 9 B 269 GLN THR HIS PHE THR ILE GLY ASP GLU VAL ILE ALA THR SEQRES 10 B 269 ALA ASP ASP ASN THR LYS ILE LEU THR VAL ARG VAL ASN SEQRES 11 B 269 GLY GLU VAL VAL LYS SER MET PRO THR SER MET GLY LYS SEQRES 12 B 269 ASP SER THR PRO THR ALA ASN GLY ILE TYR ILE VAL GLY SEQRES 13 B 269 SER ARG TYR LYS HIS ILE ILE MET ASP SER SER THR TYR SEQRES 14 B 269 GLY VAL PRO VAL ASN SER PRO ASN GLY TYR ARG THR ASP SEQRES 15 B 269 VAL ASP TRP ALA THR GLN ILE SER TYR SER GLY VAL PHE SEQRES 16 B 269 VAL HIS SER ALA PRO TRP SER VAL GLY ALA GLN GLY HIS SEQRES 17 B 269 THR ASN THR SER HIS GLY CYS LEU ASN VAL SER PRO SER SEQRES 18 B 269 ASN ALA GLN TRP PHE TYR ASP HIS VAL LYS ARG GLY ASP SEQRES 19 B 269 ILE VAL GLU VAL VAL ASN THR VAL GLY GLY THR LEU PRO SEQRES 20 B 269 GLY ILE ASP GLY LEU GLY ASP TRP ASN ILE PRO TRP ASP SEQRES 21 B 269 GLN TRP ARG ALA GLY ASN ALA LYS ALA HET 2RG A 501 33 HET GOL A 502 14 HET GOL A 503 14 HET GOL A 504 14 HET 2RG B 501 33 HET GOL B 502 14 HET ACY B 503 7 HETNAM 2RG (2S,3R,4S)-4-({(3S,5S)-5-[(3-CARBOXYPHENYL) HETNAM 2 2RG CARBAMOYL]PYRROLIDIN-3-YL}SULFANYL)-2-[(1S,2R)-1- HETNAM 3 2RG FORMYL-2-HYDROXYPROPYL]-3-METHYL-3,4-DIHYDRO-2H- HETNAM 4 2RG PYRROLE-5-CARBOXYLIC ACID HETNAM GOL GLYCEROL HETNAM ACY ACETIC ACID HETSYN 2RG ERTAPENEM, BOUND FORM POST-ISOMERIZED HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 2RG 2(C22 H27 N3 O7 S) FORMUL 4 GOL 4(C3 H8 O3) FORMUL 9 ACY C2 H4 O2 FORMUL 10 HOH *402(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 VAL A 342 5 4 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 2 LEU A 151 THR A 152 0 SHEET 2 AA1 2 PHE A 238 GLY A 239 1 O PHE A 238 N THR A 152 SHEET 1 AA2 4 PRO A 154 MET A 157 0 SHEET 2 AA2 4 VAL A 170 PHE A 174 -1 O ALA A 171 N MET A 157 SHEET 3 AA2 4 GLU A 207 PRO A 212 -1 O TRP A 210 N VAL A 170 SHEET 4 AA2 4 GLY A 198 TRP A 202 -1 N TYR A 201 O ARG A 209 SHEET 1 AA3 4 VAL A 163 VAL A 164 0 SHEET 2 AA3 4 VAL A 243 ILE A 249 1 O THR A 248 N VAL A 164 SHEET 3 AA3 4 ALA A 221 VAL A 226 -1 N VAL A 224 O THR A 245 SHEET 4 AA3 4 ILE A 188 ASN A 193 -1 N THR A 191 O ASP A 223 SHEET 1 AA4 5 GLU A 271 PRO A 277 0 SHEET 2 AA4 5 ILE A 263 VAL A 268 -1 N LEU A 264 O MET A 276 SHEET 3 AA4 5 VAL A 253 ASP A 258 -1 N THR A 256 O THR A 265 SHEET 4 AA4 5 ILE A 374 VAL A 378 1 O ILE A 374 N ALA A 255 SHEET 5 AA4 5 GLY A 290 ILE A 293 -1 N TYR A 292 O VAL A 375 SHEET 1 AA5 4 ARG A 297 ASP A 304 0 SHEET 2 AA5 4 ARG A 319 GLN A 327 -1 O THR A 320 N MET A 303 SHEET 3 AA5 4 PHE A 334 SER A 337 -1 O VAL A 335 N THR A 326 SHEET 4 AA5 4 LEU A 355 VAL A 357 1 O LEU A 355 N PHE A 334 SHEET 1 AA6 2 LEU B 151 THR B 152 0 SHEET 2 AA6 2 PHE B 238 GLY B 239 1 O PHE B 238 N THR B 152 SHEET 1 AA7 4 PRO B 154 MET B 157 0 SHEET 2 AA7 4 VAL B 170 PHE B 174 -1 O ARG B 173 N TYR B 155 SHEET 3 AA7 4 GLU B 207 PRO B 212 -1 O TRP B 210 N VAL B 170 SHEET 4 AA7 4 GLY B 198 TRP B 202 -1 N TYR B 201 O ARG B 209 SHEET 1 AA8 4 GLU B 162 VAL B 164 0 SHEET 2 AA8 4 VAL B 243 ILE B 249 1 O THR B 248 N VAL B 164 SHEET 3 AA8 4 ALA B 221 VAL B 226 -1 N VAL B 226 O VAL B 243 SHEET 4 AA8 4 ILE B 188 ASN B 193 -1 N THR B 191 O ASP B 223 SHEET 1 AA9 5 GLU B 271 PRO B 277 0 SHEET 2 AA9 5 ILE B 263 VAL B 268 -1 N LEU B 264 O MET B 276 SHEET 3 AA9 5 VAL B 253 ASP B 258 -1 N THR B 256 O THR B 265 SHEET 4 AA9 5 ILE B 374 VAL B 378 1 O GLU B 376 N ALA B 257 SHEET 5 AA9 5 GLY B 290 ILE B 293 -1 N TYR B 292 O VAL B 375 SHEET 1 AB1 4 ARG B 297 ASP B 304 0 SHEET 2 AB1 4 ARG B 319 GLN B 327 -1 O THR B 320 N MET B 303 SHEET 3 AB1 4 PHE B 334 SER B 337 -1 O VAL B 335 N THR B 326 SHEET 4 AB1 4 LEU B 355 VAL B 357 1 O LEU B 355 N PHE B 334 LINK SG CYS A 354 CAA 2RG A 501 1555 1555 1.80 LINK SG CYS B 354 CAA 2RG B 501 1555 1555 1.78 CISPEP 1 MET A 157 PRO A 158 0 0.03 CISPEP 2 ASN A 193 PRO A 194 0 -0.57 CISPEP 3 MET B 157 PRO B 158 0 0.69 CISPEP 4 ASN B 193 PRO B 194 0 -0.18 SITE 1 AC1 10 MET A 303 TYR A 308 TYR A 318 SER A 331 SITE 2 AC1 10 GLY A 332 HIS A 352 CYS A 354 TRP B 324 SITE 3 AC1 10 GLN B 363 ASP B 367 SITE 1 AC2 6 ILE A 188 LYS A 189 ILE A 190 GLY A 198 SITE 2 AC2 6 PHE A 200 TRP A 210 SITE 1 AC3 4 GLU A 213 HIS A 214 PHE A 215 ILE A 291 SITE 1 AC4 6 LYS A 299 TRP A 324 GLN A 363 ASP A 367 SITE 2 AC4 6 HOH A 608 2RG B 501 SITE 1 AC5 5 GLU B 213 HIS B 214 PHE B 215 ILE B 291 SITE 2 AC5 5 HOH B 601 SITE 1 AC6 6 GLU B 168 ALA B 171 ARG B 209 ARG B 371 SITE 2 AC6 6 HOH B 634 HOH B 672 SITE 1 AC7 19 LYS A 299 GLN A 363 GOL A 504 HOH A 608 SITE 2 AC7 19 SER B 279 MET B 303 TYR B 308 VAL B 310 SITE 3 AC7 19 TYR B 318 GLY B 332 PHE B 334 HIS B 336 SITE 4 AC7 19 SER B 351 HIS B 352 GLY B 353 LEU B 355 SITE 5 AC7 19 ASN B 356 HOH B 630 HOH B 671 CRYST1 68.181 73.207 103.803 90.00 90.00 90.00 P 21 21 21 8 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 0.014667 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013660 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009634 0.00000