HEADER TRANSFERASE 06-NOV-02 1N5J TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE TITLE 2 COMPLEXED WITH THYMIDINE DIPHOSPHATE (TDP) AND THYMIDINE TRIPHOSPHATE TITLE 3 (TTP) AT PH 5.4 (1.85 A RESOLUTION) COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDYLATE KINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.4.9; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS TRANSFERASE (ATP:TMP PHOSPHOTRANSFERASE), KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.FIORAVANTI,A.HAOUZ,T.URSBY,H.MUNIER-LEHMANN,M.DELARUE,D.BOURGEOIS REVDAT 3 14-FEB-24 1N5J 1 REMARK LINK REVDAT 2 24-FEB-09 1N5J 1 VERSN REVDAT 1 15-APR-03 1N5J 0 JRNL AUTH E.FIORAVANTI,A.HAOUZ,T.URSBY,H.MUNIER-LEHMANN,M.DELARUE, JRNL AUTH 2 D.BOURGEOIS JRNL TITL MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE: STRUCTURAL JRNL TITL 2 STUDIES OF INTERMEDIATES ALONG THE REACTION PATHWAY JRNL REF J.MOL.BIOL. V. 327 1077 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12662932 JRNL DOI 10.1016/S0022-2836(03)00202-X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.URSBY,M.WEIK,E.FIORAVANTI,M.DELARUE,M.GOELDNER,D.BOURGEOIS REMARK 1 TITL CRYO-PHOTOLYSIS OF CAGED COMPOUNDS: A TECHNIQUE FOR TRAPPING REMARK 1 TITL 2 INTERMEDIATE STATES IN PROTEIN CRYSTALS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 58 607 2002 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444902002135 REMARK 1 REFERENCE 2 REMARK 1 AUTH I.LI DE LA SIERRA,H.MUNIER-LEHMANN,A.M.GILLES,O.BARZU, REMARK 1 AUTH 2 M.DELARUE REMARK 1 TITL X-RAY STRUCTURE OF TMP KINASE FROM MYCOBACTERIUM REMARK 1 TITL 2 TUBERCULOSIS COMPLEXED WITH TMP AT 1.95 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 311 87 2001 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.2001.4843 REMARK 1 REFERENCE 3 REMARK 1 AUTH I.LI DE LA SIERRA,H.MUNIER-LEHMANN,A.M.GILLES,O.BARZU, REMARK 1 AUTH 2 M.DELARUE REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF THE REMARK 1 TITL 2 THYMIDYLATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 56 226 2000 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444999016212 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2014027.220 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 19047 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 929 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3026 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 152 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1529 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.88000 REMARK 3 B22 (A**2) : 1.88000 REMARK 3 B33 (A**2) : -3.77000 REMARK 3 B12 (A**2) : 2.08000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.14 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.730 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.040 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.500 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.890 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.660 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 45.94 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : TMP_TDP_TTP_MOD.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : TMP_TDP_TTP_MOD.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE CONTAINS TWO REMARK 3 CONFORMATIONS: CONFORMATION A CORRESPONDS TO THE TYD-BOUND REMARK 3 STATE. CONFORMATION B CORRESPONDS TO THE TTP-BOUND STATE. REMARK 4 REMARK 4 1N5J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-02. REMARK 100 THE DEPOSITION ID IS D_1000017544. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19063 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 24.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.31600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: CNS 1.0 REMARK 200 STARTING MODEL: 1GSI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SOAKING IN 30MM ATP, 40% PEG 2000, 10 REMARK 280 MM AMMONIUM SULPHATE, 0.1 M MES PH 5.4, 25 MM MAGNESIUM ACETATE, REMARK 280 2 MM MERCAPTOETHANOL, 3 MM EDTA, 1.5 MM DTT, VAPOR DIFFUSION, REMARK 280 HANGING DROP + SOAKING, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 90.07600 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 45.03800 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 67.55700 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 22.51900 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 112.59500 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 90.07600 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 45.03800 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 22.51900 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 67.55700 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 112.59500 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER GENERATED FROM THE REMARK 300 MONOMER IN THE ASYMMETRIC UNIT BY THE OPERATIONS: X-Y, -Y, -Z. 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: DIMERIC 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 PRO A 209 REMARK 465 PRO A 210 REMARK 465 ASP A 211 REMARK 465 VAL A 212 REMARK 465 PRO A 213 REMARK 465 SER A 214 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 GLU A 18 CG CD OE1 OE2 REMARK 470 LYS A 19 CD CE NZ REMARK 470 ARG A 29 NE CZ NH1 NH2 REMARK 470 ARG A 86 CD NE CZ NH1 NH2 REMARK 470 GLU A 144 CG CD OE1 OE2 REMARK 470 LEU A 145 CG CD1 CD2 REMARK 470 GLU A 148 CD OE1 OE2 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 ARG A 95 144.29 81.13 REMARK 500 TYR A 96 -151.58 -154.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 217 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 9 OD1 REMARK 620 2 GLU A 166 OE1 99.2 REMARK 620 3 TYD A 218 O2A 75.3 172.3 REMARK 620 4 TYD A 218 O2B 161.0 99.8 85.7 REMARK 620 5 HOH A1009 O 86.3 89.8 95.1 94.1 REMARK 620 6 HOH A1018 O 86.3 84.0 90.2 95.2 169.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 217 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 9 OD1 REMARK 620 2 GLU A 166 OE1 105.3 REMARK 620 3 TTP A 219 O2A 84.6 167.6 REMARK 620 4 TTP A 219 O2B 153.3 100.5 70.7 REMARK 620 5 HOH A1009 O 85.4 81.9 106.7 91.9 REMARK 620 6 HOH A1018 O 102.6 84.9 85.7 86.0 166.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TTP A 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYD A 218 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GSI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE REMARK 900 COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) AND MAGNESIUM (1.6 A REMARK 900 RESOLUTION) REMARK 900 RELATED ID: 1G3U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE REMARK 900 COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) AND MAGNESIUM (1.95 A REMARK 900 RESOLUTION) REMARK 900 RELATED ID: 1N5K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE REMARK 900 CRYSTALLIZED IN SODIUM MALONATE (RESOLUTION 2.1 A) REMARK 900 RELATED ID: 1N5I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF INACTIVE MYCOBACTERIUM TUBERCULOSIS REMARK 900 THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) AT REMARK 900 PH 4.6 (RESOLUTION 1.85 A) REMARK 900 RELATED ID: 1N5L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE REMARK 900 CRYSTALLIZED IN SODIUM MALONATE, AFTER CATALYSIS IN THE CRYSTAL REMARK 900 (2.3 A RESOLUTION) DBREF 1N5J A 1 208 UNP O05891 KTHY_MYCTU 1 208 SEQRES 1 A 214 MET LEU ILE ALA ILE GLU GLY VAL ASP GLY ALA GLY LYS SEQRES 2 A 214 ARG THR LEU VAL GLU LYS LEU SER GLY ALA PHE ARG ALA SEQRES 3 A 214 ALA GLY ARG SER VAL ALA THR LEU ALA PHE PRO ARG TYR SEQRES 4 A 214 GLY GLN SER VAL ALA ALA ASP ILE ALA ALA GLU ALA LEU SEQRES 5 A 214 HIS GLY GLU HIS GLY ASP LEU ALA SER SER VAL TYR ALA SEQRES 6 A 214 MET ALA THR LEU PHE ALA LEU ASP ARG ALA GLY ALA VAL SEQRES 7 A 214 HIS THR ILE GLN GLY LEU CYS ARG GLY TYR ASP VAL VAL SEQRES 8 A 214 ILE LEU ASP ARG TYR VAL ALA SER ASN ALA ALA TYR SER SEQRES 9 A 214 ALA ALA ARG LEU HIS GLU ASN ALA ALA GLY LYS ALA ALA SEQRES 10 A 214 ALA TRP VAL GLN ARG ILE GLU PHE ALA ARG LEU GLY LEU SEQRES 11 A 214 PRO LYS PRO ASP TRP GLN VAL LEU LEU ALA VAL SER ALA SEQRES 12 A 214 GLU LEU ALA GLY GLU ARG SER ARG GLY ARG ALA GLN ARG SEQRES 13 A 214 ASP PRO GLY ARG ALA ARG ASP ASN TYR GLU ARG ASP ALA SEQRES 14 A 214 GLU LEU GLN GLN ARG THR GLY ALA VAL TYR ALA GLU LEU SEQRES 15 A 214 ALA ALA GLN GLY TRP GLY GLY ARG TRP LEU VAL VAL GLY SEQRES 16 A 214 ALA ASP VAL ASP PRO GLY ARG LEU ALA ALA THR LEU ALA SEQRES 17 A 214 PRO PRO ASP VAL PRO SER HET SO4 A 215 5 HET SO4 A 216 5 HET MG A 217 2 HET TYD A 218 25 HET TTP A 219 29 HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETNAM TYD THYMIDINE-5'-DIPHOSPHATE HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 MG MG 2+ FORMUL 5 TYD C10 H16 N2 O11 P2 FORMUL 6 TTP C10 H17 N2 O14 P3 FORMUL 7 HOH *154(H2 O) HELIX 1 1 GLY A 12 ALA A 27 1 16 HELIX 2 2 SER A 42 HIS A 53 1 12 HELIX 3 3 ASP A 58 SER A 61 5 4 HELIX 4 4 SER A 62 GLY A 76 1 15 HELIX 5 5 ALA A 77 TYR A 88 1 12 HELIX 6 6 TYR A 96 LEU A 108 1 13 HELIX 7 7 GLY A 114 PHE A 125 1 12 HELIX 8 8 SER A 142 ASP A 157 1 16 HELIX 9 9 PRO A 158 ALA A 161 5 4 HELIX 10 10 ASP A 168 GLY A 186 1 19 HELIX 11 11 ASP A 199 ALA A 208 1 10 SHEET 1 A 5 VAL A 31 ALA A 35 0 SHEET 2 A 5 VAL A 90 ASP A 94 1 O ILE A 92 N ALA A 32 SHEET 3 A 5 LEU A 2 GLU A 6 1 N ILE A 3 O LEU A 93 SHEET 4 A 5 TRP A 135 LEU A 139 1 O VAL A 137 N GLU A 6 SHEET 5 A 5 ARG A 190 VAL A 194 1 O LEU A 192 N LEU A 138 LINK OD1 ASP A 9 MG A MG A 217 1555 1555 2.40 LINK OD1 ASP A 9 MG B MG A 217 1555 1555 2.16 LINK OE1 GLU A 166 MG A MG A 217 1555 1555 2.22 LINK OE1 GLU A 166 MG B MG A 217 1555 1555 2.27 LINK MG A MG A 217 O2AATYD A 218 1555 1555 2.09 LINK MG A MG A 217 O2BATYD A 218 1555 1555 1.96 LINK MG B MG A 217 O2ABTTP A 219 1555 1555 2.43 LINK MG B MG A 217 O2BBTTP A 219 1555 1555 2.39 LINK MG A MG A 217 O AHOH A1009 1555 1555 1.95 LINK MG B MG A 217 O BHOH A1009 1555 1555 2.55 LINK MG A MG A 217 O AHOH A1018 1555 1555 2.16 LINK MG B MG A 217 O BHOH A1018 1555 1555 2.56 CISPEP 1 PHE A 36 PRO A 37 0 0.10 SITE 1 AC1 6 ASP A 9 GLU A 166 TYD A 218 TTP A 219 SITE 2 AC1 6 HOH A1009 HOH A1018 SITE 1 AC2 9 GLY A 10 GLY A 12 LYS A 13 ARG A 14 SITE 2 AC2 9 ARG A 153 HOH A1014 HOH A1027 HOH A1041 SITE 3 AC2 9 HOH A1140 SITE 1 AC3 4 ALA A 154 ARG A 162 ARG A 167 HOH A1030 SITE 1 AC4 21 ASP A 9 ARG A 14 PRO A 37 TYR A 39 SITE 2 AC4 21 PHE A 70 ARG A 74 ARG A 95 ASN A 100 SITE 3 AC4 21 TYR A 103 TYR A 165 MG A 217 HOH A1002 SITE 4 AC4 21 HOH A1009 HOH A1014 HOH A1018 HOH A1046 SITE 5 AC4 21 HOH A1119 HOH A1128 HOH A1140 HOH A1151 SITE 6 AC4 21 HOH A1234 SITE 1 AC5 17 ASP A 9 TYR A 39 PHE A 70 ARG A 74 SITE 2 AC5 17 ARG A 95 ASN A 100 TYR A 165 GLU A 166 SITE 3 AC5 17 MG A 217 HOH A1002 HOH A1009 HOH A1014 SITE 4 AC5 17 HOH A1018 HOH A1046 HOH A1119 HOH A1151 SITE 5 AC5 17 HOH A1234 CRYST1 76.248 76.248 135.114 90.00 90.00 120.00 P 65 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 0.013115 0.007572 0.000000 0.00000 SCALE2 0.000000 0.015144 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007401 0.00000