HEADER TRANSFERASE 06-APR-15 4Z7A TITLE STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF A NON-FUNCTIONALLY TITLE 2 REDUNDANT M. TUBERCULOSIS (3,3) L,D-TRANSPEPTIDASE, LDTMT5. COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYCOBACTERIUM TUBERCULOSIS (3,3)L,D-TRANSPEPTIDASE TYPE 5; COMPND 3 CHAIN: A; COMPND 4 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: LPRQ, MRA_0490; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS PEPTIDOGLYCAN, CELL WALL BIOSYNTHESIS, CARBAPENEMS, NITROCEFIN, KEYWDS 2 ENZYME KINETICS, ENZYME STRUCTURE, ANTIBIOTICS, CELL WALL, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.BASTA,A.GHOSH,Y.PAN,J.JAKONCIC,E.LLOYD,G.TOWNSEND,G.LAMICHHANE, AUTHOR 2 M.A.BIANCHET REVDAT 4 27-SEP-23 4Z7A 1 JRNL REMARK REVDAT 3 28-OCT-15 4Z7A 1 JRNL REVDAT 2 09-SEP-15 4Z7A 1 JRNL REVDAT 1 02-SEP-15 4Z7A 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. 1.98 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 40931 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2040 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 28.9252 - 4.8759 0.99 2840 159 0.1809 0.2220 REMARK 3 2 4.8759 - 3.8731 1.00 2680 135 0.1627 0.1893 REMARK 3 3 3.8731 - 3.3843 0.99 2653 126 0.2083 0.2636 REMARK 3 4 3.3843 - 3.0753 1.00 2618 145 0.2289 0.2965 REMARK 3 5 3.0753 - 2.8551 0.99 2595 146 0.2570 0.3125 REMARK 3 6 2.8551 - 2.6869 0.99 2565 141 0.2627 0.2840 REMARK 3 7 2.6869 - 2.5524 0.99 2586 126 0.2556 0.3028 REMARK 3 8 2.5524 - 2.4413 1.00 2566 138 0.2655 0.2878 REMARK 3 9 2.4413 - 2.3474 1.00 2554 134 0.2706 0.3238 REMARK 3 10 2.3474 - 2.2664 0.99 2558 136 0.2753 0.3231 REMARK 3 11 2.2664 - 2.1956 0.99 2530 133 0.2928 0.3250 REMARK 3 12 2.1956 - 2.1329 0.99 2558 138 0.2730 0.3153 REMARK 3 13 2.1329 - 2.0767 0.99 2566 110 0.2782 0.3135 REMARK 3 14 2.0767 - 2.0261 0.99 2528 140 0.3177 0.3040 REMARK 3 15 2.0261 - 1.9800 0.98 2494 133 0.3069 0.3862 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.490 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 : 0.006 2838 REMARK 3 ANGLE : 1.071 3881 REMARK 3 CHIRALITY : 0.038 421 REMARK 3 PLANARITY : 0.005 509 REMARK 3 DIHEDRAL : 13.169 1002 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 56 THROUGH 154) REMARK 3 ORIGIN FOR THE GROUP (A): -42.8519 -12.9642 -26.0427 REMARK 3 T TENSOR REMARK 3 T11: 0.8103 T22: 0.6435 REMARK 3 T33: 0.4730 T12: 0.2106 REMARK 3 T13: -0.0479 T23: 0.0841 REMARK 3 L TENSOR REMARK 3 L11: 0.3009 L22: 0.3313 REMARK 3 L33: 0.4838 L12: 0.0192 REMARK 3 L13: 0.1008 L23: -0.6030 REMARK 3 S TENSOR REMARK 3 S11: -0.0542 S12: -0.3700 S13: -0.1132 REMARK 3 S21: 0.3839 S22: -0.0543 S23: -0.0012 REMARK 3 S31: -0.5091 S32: -0.2994 S33: 0.0004 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 155 THROUGH 261) REMARK 3 ORIGIN FOR THE GROUP (A): -20.1203 -26.1428 0.7938 REMARK 3 T TENSOR REMARK 3 T11: 0.4267 T22: 0.4690 REMARK 3 T33: 0.4049 T12: -0.0789 REMARK 3 T13: -0.1818 T23: 0.0943 REMARK 3 L TENSOR REMARK 3 L11: 1.5581 L22: 0.3430 REMARK 3 L33: 0.7671 L12: -0.2005 REMARK 3 L13: 0.4864 L23: 0.2199 REMARK 3 S TENSOR REMARK 3 S11: -0.3770 S12: 0.2408 S13: 0.1949 REMARK 3 S21: -0.0519 S22: -0.0390 S23: 0.0197 REMARK 3 S31: -0.5811 S32: 0.1387 S33: -0.3753 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 262 THROUGH 387 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.5379 -42.1794 14.3852 REMARK 3 T TENSOR REMARK 3 T11: 0.1960 T22: 0.7744 REMARK 3 T33: 0.4432 T12: -0.0776 REMARK 3 T13: -0.0684 T23: -0.0219 REMARK 3 L TENSOR REMARK 3 L11: 0.3015 L22: 0.3604 REMARK 3 L33: 0.5327 L12: 0.5869 REMARK 3 L13: 0.3287 L23: 0.0879 REMARK 3 S TENSOR REMARK 3 S11: -0.2161 S12: 0.1040 S13: -0.2003 REMARK 3 S21: 0.1033 S22: 0.2139 S23: -0.1323 REMARK 3 S31: -0.1650 S32: 0.4733 S33: -0.0298 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 388 THROUGH 416) REMARK 3 ORIGIN FOR THE GROUP (A): -12.5525 -22.4591 12.9177 REMARK 3 T TENSOR REMARK 3 T11: 0.7241 T22: 0.5276 REMARK 3 T33: 0.5851 T12: -0.1711 REMARK 3 T13: -0.3025 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 0.0758 L22: 0.0732 REMARK 3 L33: 0.2525 L12: 0.1053 REMARK 3 L13: -0.0998 L23: -0.1554 REMARK 3 S TENSOR REMARK 3 S11: -0.4380 S12: -0.1027 S13: 0.3611 REMARK 3 S21: 0.2290 S22: -0.0611 S23: -0.2398 REMARK 3 S31: -0.9538 S32: 0.4313 S33: -0.0356 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 4Z7A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : MONOCROMATOR 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 : 41222 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 57.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.90000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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: 3TUR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: GROWTH IN A WEEK, VAPOR DIFFUSION, REMARK 280 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 128.49867 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 64.24933 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 128.49867 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 64.24933 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 128.49867 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 64.24933 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 128.49867 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 64.24933 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 SER A 347 REMARK 465 ALA A 348 REMARK 465 GLY A 349 REMARK 465 ALA A 350 REMARK 465 GLN A 351 REMARK 465 GLY A 352 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 CD1 CE1 CE2 CZ 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 OD2 ASP A 113 OG1 THR A 115 2.07 REMARK 500 O HOH A 724 O HOH A 745 2.11 REMARK 500 O HOH A 735 O HOH A 737 2.19 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 ALA A 57 -105.11 59.07 REMARK 500 GLU A 58 76.95 53.83 REMARK 500 HIS A 272 15.43 58.15 REMARK 500 THR A 278 -167.87 -126.33 REMARK 500 THR A 308 -85.72 -118.08 REMARK 500 PHE A 314 74.13 177.98 REMARK 500 HIS A 325 47.24 -161.01 REMARK 500 ASN A 358 -107.87 -69.18 REMARK 500 PRO A 414 -157.00 -65.82 REMARK 500 PRO A 415 -72.30 -69.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 761 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A 762 DISTANCE = 6.41 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 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 PGE A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACE A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TUR RELATED DB: PDB REMARK 900 PARALOG IN COMPLEX WITH APEPTIDOGLYCAN STEM FRAGMENT REMARK 900 RELATED ID: 3U1Q RELATED DB: PDB REMARK 900 PARALOG IN COMPLEX WITH BETA-MERCAPTOETHANOL REMARK 900 RELATED ID: 3VAE RELATED DB: PDB REMARK 900 PARALOG WITH THE CATALYTIC CYSTEINE OXIDATED REMARK 900 RELATED ID: 3U1P RELATED DB: PDB REMARK 900 RELATED ID: 3TX4 RELATED DB: PDB REMARK 900 MTB. PARALOG WITH TTHE CATALYTIC CYSTEINE MUTATED DBREF 4Z7A A 1 451 UNP A5TZL1 A5TZL1_MYCTA 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 PO4 A 501 5 HET PEG A 502 17 HET PGE A 503 24 HET ACE A 504 7 HETNAM PO4 PHOSPHATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PGE TRIETHYLENE GLYCOL HETNAM ACE ACETYL GROUP FORMUL 2 PO4 O4 P 3- FORMUL 3 PEG C4 H10 O3 FORMUL 4 PGE C6 H14 O4 FORMUL 5 ACE C2 H4 O FORMUL 6 HOH *162(H2 O) HELIX 1 AA1 ASP A 186 ARG A 192 1 7 HELIX 2 AA2 LEU A 295 VAL A 299 5 5 HELIX 3 AA3 SER A 364 ALA A 375 1 12 HELIX 4 AA4 SER A 391 GLY A 395 5 5 HELIX 5 AA5 TRP A 398 VAL A 402 5 5 HELIX 6 AA6 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 GLY A 137 -1 N TYR A 129 O PHE A 149 SHEET 4 AA2 5 GLY A 91 ASN A 100 -1 N GLN A 94 O SER A 134 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 GLY A 137 -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 LYS A 156 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 PHE A 243 O ALA A 247 SHEET 1 AA5 4 ALA A 160 PHE A 162 0 SHEET 2 AA5 4 VAL A 176 PHE A 180 -1 O GLN A 179 N GLY A 161 SHEET 3 AA5 4 ARG A 217 PRO A 222 -1 O VAL A 218 N ILE A 178 SHEET 4 AA5 4 GLY A 204 LEU A 209 -1 N ALA A 207 O HIS A 219 SHEET 1 AA6 4 THR A 169 VAL A 170 0 SHEET 2 AA6 4 MET A 253 ILE A 259 1 O GLN A 258 N VAL A 170 SHEET 3 AA6 4 THR A 231 ALA A 236 -1 N ALA A 236 O MET A 253 SHEET 4 AA6 4 LEU A 194 ASP A 199 -1 N THR A 197 O ASP A 233 SHEET 1 AA7 5 GLY A 281 PRO A 287 0 SHEET 2 AA7 5 ARG A 273 THR A 278 -1 N ILE A 274 O PHE A 286 SHEET 3 AA7 5 GLN A 263 GLU A 268 -1 N VAL A 264 O VAL A 277 SHEET 4 AA7 5 PRO A 380 THR A 384 1 O GLU A 382 N VAL A 265 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 ASP A 313 0 SHEET 2 AA8 4 ARG A 329 ARG A 333 -1 O ALA A 331 N TYR A 311 SHEET 3 AA8 4 PHE A 340 ALA A 343 -1 O ILE A 341 N VAL A 332 SHEET 4 AA8 4 ILE A 361 LEU A 363 1 O ILE A 361 N PHE A 340 CISPEP 1 ARG A 70 PRO A 71 0 4.83 CISPEP 2 ASP A 199 PRO A 200 0 5.15 CISPEP 3 ASP A 396 ILE A 397 0 -10.72 CISPEP 4 PRO A 415 PRO A 416 0 5.43 SITE 1 AC1 4 GLY A 147 GLU A 268 THR A 384 HOH A 611 SITE 1 AC2 5 PRO A 122 LEU A 123 TYR A 239 HOH A 601 SITE 2 AC2 5 HOH A 748 SITE 1 AC3 6 GLU A 309 LYS A 310 PHE A 314 TYR A 315 SITE 2 AC3 6 MET A 316 TYR A 372 SITE 1 AC4 3 ASN A 100 LYS A 104 TYR A 129 CRYST1 101.026 101.026 192.748 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 0.009898 0.005715 0.000000 0.00000 SCALE2 0.000000 0.011430 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005188 0.00000