HEADER TRANSFERASE 06-NOV-02 1N5L
TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE
TITLE 2 CRYSTALLIZED IN SODIUM MALONATE, AFTER CATALYSIS IN THE CRYSTAL (2.3
TITLE 3 A RESOLUTION)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: THYMIDYLATE KINASE;
COMPND 3 CHAIN: A, B;
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 4 14-FEB-24 1N5L 1 REMARK
REVDAT 3 31-JAN-18 1N5L 1 REMARK
REVDAT 2 24-FEB-09 1N5L 1 VERSN
REVDAT 1 15-APR-03 1N5L 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. 375 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. 2.30 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) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.76
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1848944.310
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1
REMARK 3 NUMBER OF REFLECTIONS : 21577
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) : 0.236
REMARK 3 FREE R VALUE : 0.280
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 1054
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009
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) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3345
REMARK 3 BIN R VALUE (WORKING SET) : 0.2470
REMARK 3 BIN FREE R VALUE : 0.3090
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 165
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2905
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 63
REMARK 3 SOLVENT ATOMS : 205
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 41.00
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.90
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 6.08000
REMARK 3 B22 (A**2) : 6.08000
REMARK 3 B33 (A**2) : -12.17000
REMARK 3 B12 (A**2) : 4.70000
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) : 0.29
REMARK 3 ESD FROM SIGMAA (A) : -0.0
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) : 0.36
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.500
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.00
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.090
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) : 3.410 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.310 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 5.060 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.320 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.35
REMARK 3 BSOL : 63.18
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+ACT+DPO.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+ACT+DPO.TOP
REMARK 3 TOPOLOGY FILE 5 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: MONOMER A CONTAINS THE APO-STRUCTURE.
REMARK 3 MONOMER B CONTAINS THE TDP-MG++-ADP COMPLEX.
REMARK 4
REMARK 4 1N5L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-02.
REMARK 100 THE DEPOSITION ID IS D_1000017546.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-APR-01
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID29
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.936
REMARK 200 MONOCHROMATOR : SILICON
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA)
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21648
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 19.760
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 200 DATA REDUNDANCY : 6.900
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.10700
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 7.20
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.38100
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900
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: PDB ENTRY 1N5K
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.12
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M SODIUM MALONATE, 2% PEG 2000,
REMARK 280 0.1 M MES PH 6.0, 2 MM B-MERCAPTOETHANOL, 25 MM MAGNESIUM
REMARK 280 ACETATE, SOAKING IN 30 MM ATP, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 STREAK SEEDING, SOAKING, TEMPERATURE 293.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+2/3
REMARK 290 6555 -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 65.29967
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 130.59933
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 130.59933
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 65.29967
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 ASYMMETRIC UNIT CONTAINS THE FUNCTIONAL DIMER.
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, 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 SER A 150
REMARK 465 ARG A 151
REMARK 465 GLY A 152
REMARK 465 ARG A 153
REMARK 465 ALA A 154
REMARK 465 GLN A 155
REMARK 465 ARG A 156
REMARK 465 ASP A 157
REMARK 465 PRO A 158
REMARK 465 GLY A 159
REMARK 465 ARG A 160
REMARK 465 ALA A 161
REMARK 465 ARG A 162
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 465 GLN B 155
REMARK 465 ARG B 156
REMARK 465 ASP B 157
REMARK 465 PRO B 158
REMARK 465 GLY B 159
REMARK 465 PRO B 209
REMARK 465 PRO B 210
REMARK 465 ASP B 211
REMARK 465 VAL B 212
REMARK 465 PRO B 213
REMARK 465 SER B 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 ASP A 9 CG OD1 OD2
REMARK 470 ARG A 14 CD NE CZ NH1 NH2
REMARK 470 GLU A 55 OE1 OE2
REMARK 470 GLU A 144 CG CD OE1 OE2
REMARK 470 GLU A 148 CG CD OE1 OE2
REMARK 470 ASN A 164 CG OD1 ND2
REMARK 470 GLU A 166 CG CD OE1 OE2
REMARK 470 ARG A 167 CG CD NE CZ NH1 NH2
REMARK 470 LEU A 171 CG CD1 CD2
REMARK 470 ARG A 190 CG CD NE CZ NH1 NH2
REMARK 470 ARG B 86 CG CD NE CZ NH1 NH2
REMARK 470 ARG B 153 CG CD NE CZ NH1 NH2
REMARK 470 ARG B 167 CD NE CZ NH1 NH2
REMARK 470 ARG B 190 CG CD NE CZ NH1 NH2
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 NH1 ARG B 151 O HOH B 455 2.06
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 ARG A 95 128.97 79.02
REMARK 500 TYR A 96 -153.06 -142.54
REMARK 500 ALA A 196 0.79 -64.45
REMARK 500 ARG B 95 145.43 78.56
REMARK 500 TYR B 96 -158.24 -160.06
REMARK 500 ASN B 111 -165.24 -111.95
REMARK 500 ASP B 197 35.32 -91.39
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN HOH MOLECULES 140 AND 141 WERE BOTH NAMED 140 IN THE
REMARK 600 PAPER BECAUSE THEY OCCUPY THE SAME SITE IN THE 2 MONOMERS (A AND
REMARK 600 B), IN ORDER TO MAKE AN EASIER COMPARISON OF THE ACTIVE SITES.
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 DPO B 414
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 B 215 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 9 OD1
REMARK 620 2 TYD B 216 O2B 163.4
REMARK 620 3 TYD B 216 O2A 89.1 83.9
REMARK 620 4 HOH B 469 O 72.6 92.3 89.7
REMARK 620 5 HOH B 502 O 88.8 102.2 67.7 151.3
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 215
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 412
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 413
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TMP A 409
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYD B 216
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DPO B 414
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1N5K RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE
REMARK 900 CRYSTALLIZED IN SODIUM MALONATE (2.1 A RESOLUTION)
REMARK 900 RELATED ID: 1GTV RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE
REMARK 900 COMPLEXED WITH THYMIDINE-5'-DIPHOSPHATE (TDP)
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: 1N5J RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE
REMARK 900 COMPLEXED WITH THYMIDINE DIPHOSPHATE (TDP) AND THYMIDINE
REMARK 900 TRIPHOSPHATE (TTP) AT PH 5.4 (RESOLUTION 1.85 A)
DBREF 1N5L A 1 214 UNP O05891 KTHY_MYCTU 1 214
DBREF 1N5L B 1 214 PDB 1N5L 1N5L 1 214
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
SEQRES 1 B 214 MET LEU ILE ALA ILE GLU GLY VAL ASP GLY ALA GLY LYS
SEQRES 2 B 214 ARG THR LEU VAL GLU LYS LEU SER GLY ALA PHE ARG ALA
SEQRES 3 B 214 ALA GLY ARG SER VAL ALA THR LEU ALA PHE PRO ARG TYR
SEQRES 4 B 214 GLY GLN SER VAL ALA ALA ASP ILE ALA ALA GLU ALA LEU
SEQRES 5 B 214 HIS GLY GLU HIS GLY ASP LEU ALA SER SER VAL TYR ALA
SEQRES 6 B 214 MET ALA THR LEU PHE ALA LEU ASP ARG ALA GLY ALA VAL
SEQRES 7 B 214 HIS THR ILE GLN GLY LEU CYS ARG GLY TYR ASP VAL VAL
SEQRES 8 B 214 ILE LEU ASP ARG TYR VAL ALA SER ASN ALA ALA TYR SER
SEQRES 9 B 214 ALA ALA ARG LEU HIS GLU ASN ALA ALA GLY LYS ALA ALA
SEQRES 10 B 214 ALA TRP VAL GLN ARG ILE GLU PHE ALA ARG LEU GLY LEU
SEQRES 11 B 214 PRO LYS PRO ASP TRP GLN VAL LEU LEU ALA VAL SER ALA
SEQRES 12 B 214 GLU LEU ALA GLY GLU ARG SER ARG GLY ARG ALA GLN ARG
SEQRES 13 B 214 ASP PRO GLY ARG ALA ARG ASP ASN TYR GLU ARG ASP ALA
SEQRES 14 B 214 GLU LEU GLN GLN ARG THR GLY ALA VAL TYR ALA GLU LEU
SEQRES 15 B 214 ALA ALA GLN GLY TRP GLY GLY ARG TRP LEU VAL VAL GLY
SEQRES 16 B 214 ALA ASP VAL ASP PRO GLY ARG LEU ALA ALA THR LEU ALA
SEQRES 17 B 214 PRO PRO ASP VAL PRO SER
HET ACT A 412 4
HET ACT A 413 4
HET TMP A 409 21
HET MG B 215 1
HET TYD B 216 25
HET DPO B 414 8
HETNAM ACT ACETATE ION
HETNAM TMP THYMIDINE-5'-PHOSPHATE
HETNAM MG MAGNESIUM ION
HETNAM TYD THYMIDINE-5'-DIPHOSPHATE
HETNAM DPO DIPHOSPHATE
FORMUL 3 ACT 2(C2 H3 O2 1-)
FORMUL 5 TMP C10 H15 N2 O8 P
FORMUL 6 MG MG 2+
FORMUL 7 TYD C10 H16 N2 O11 P2
FORMUL 8 DPO O7 P2 4-
FORMUL 9 HOH *205(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 HIS A 109 1 14
HELIX 7 7 GLY A 114 PHE A 125 1 12
HELIX 8 8 SER A 142 ARG A 149 1 8
HELIX 9 9 ASP A 168 GLY A 186 1 19
HELIX 10 10 ASP A 199 ALA A 208 1 10
HELIX 11 11 GLY B 12 ALA B 27 1 16
HELIX 12 12 SER B 42 HIS B 53 1 12
HELIX 13 13 ASP B 58 SER B 61 5 4
HELIX 14 14 SER B 62 GLY B 76 1 15
HELIX 15 15 ALA B 77 TYR B 88 1 12
HELIX 16 16 TYR B 96 LEU B 108 1 13
HELIX 17 17 GLY B 114 ALA B 126 1 13
HELIX 18 18 SER B 142 ARG B 153 1 12
HELIX 19 19 ASP B 168 GLN B 185 1 18
HELIX 20 20 ASP B 199 ALA B 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 ALA A 4
SHEET 5 A 5 ARG A 190 VAL A 194 1 O VAL A 194 N LEU A 138
SHEET 1 B 5 VAL B 31 ALA B 35 0
SHEET 2 B 5 VAL B 90 ASP B 94 1 O ILE B 92 N ALA B 32
SHEET 3 B 5 LEU B 2 GLU B 6 1 N ILE B 5 O LEU B 93
SHEET 4 B 5 TRP B 135 LEU B 139 1 O TRP B 135 N ALA B 4
SHEET 5 B 5 TRP B 191 VAL B 194 1 O VAL B 194 N LEU B 138
LINK OD1 ASP B 9 MG MG B 215 1555 1555 2.32
LINK MG MG B 215 O2B TYD B 216 1555 1555 2.24
LINK MG MG B 215 O2A TYD B 216 1555 1555 1.96
LINK MG MG B 215 O HOH B 469 1555 1555 2.80
LINK MG MG B 215 O HOH B 502 1555 1555 2.99
CISPEP 1 PHE A 36 PRO A 37 0 -0.15
CISPEP 2 PHE B 36 PRO B 37 0 0.08
SITE 1 AC1 5 ASP B 9 GLU B 166 TYD B 216 HOH B 469
SITE 2 AC1 5 HOH B 502
SITE 1 AC2 3 ARG A 122 ARG A 127 ASN B 111
SITE 1 AC3 4 GLY A 10 ALA A 11 GLY A 12 LYS A 13
SITE 1 AC4 10 PRO A 37 TYR A 39 PHE A 70 ARG A 74
SITE 2 AC4 10 ARG A 95 ASN A 100 TYR A 103 TYR A 165
SITE 3 AC4 10 HOH A 434 HOH A 492
SITE 1 AC5 17 ASP B 9 PHE B 36 PRO B 37 TYR B 39
SITE 2 AC5 17 LEU B 52 PHE B 70 ARG B 74 ARG B 95
SITE 3 AC5 17 SER B 99 ASN B 100 TYR B 103 TYR B 165
SITE 4 AC5 17 MG B 215 HOH B 415 HOH B 427 HOH B 469
SITE 5 AC5 17 HOH B 502
SITE 1 AC6 7 GLY B 10 ALA B 11 GLY B 12 LYS B 13
SITE 2 AC6 7 ARG B 14 THR B 15 HOH B 502
CRYST1 64.454 64.454 195.899 90.00 90.00 120.00 P 31 2 1 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 0.015515 0.008958 0.000000 0.00000
SCALE2 0.000000 0.017915 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005105 0.00000
(ATOM LINES ARE NOT SHOWN.)
END