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- PDB-1g3u: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINAS... -

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Basic information

Entry
Database: PDB / ID: 1g3u
TitleCRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP)
ComponentsTHYMIDYLATE KINASE
KeywordsTRANSFERASE / TRANSFERASE (ATP:TMP PHOSPHOTRANSFERASE) / KINASE
Function / homology
Function and homology information


TMP metabolic process / dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding ...TMP metabolic process / dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-PHOSPHATE / Thymidylate kinase / Thymidylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsLi de la Sierra, I. / Munier-Lehmann, H. / Gilles, A.M. / Barzu, O. / Delarue, M.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: X-ray structure of TMP kinase from Mycobacterium tuberculosis complexed with TMP at 1.95 A resolution.
Authors: Li de la Sierra, I. / Munier-Lehmann, H. / Gilles, A.M. / Barzu, O. / Delarue, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray analysis of the thymidylate kinase from Mycobacterium tuberculosis
Authors: Li de la Sierra, I. / Munier-Lehmann, H. / Gilles, A.M. / Barzu, O. / Delarue, M.
#2: Journal: To be Published
Title: THYMIDYLATE KINASE OF MYCOBACTERIUM TUBERCULOSIS : A CHIMERA SHARING PROPERTIES COMMON TO EUKARYOTIC AND BACTERIALENZYMES
Authors: Munier-Lehmann, H. / Chaffotte, A. / Labesse, G. / Pochet, S.
History
DepositionOct 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2015
Polymers22,6631
Non-polymers5394
Water2,702150
1
A: THYMIDYLATE KINASE
hetero molecules

A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,40210
Polymers45,3252
Non-polymers1,0778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)76.622, 76.622, 134.378
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a homodimer

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Components

#1: Protein THYMIDYLATE KINASE / TMK


Mass: 22662.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PET22B / Production host: Escherichia coli (E. coli)
References: UniProt: O05891, UniProt: P9WKE1*PLUS, dTMP kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 2000, ammonium sulfate, magnesium acetate, beta-mercaptoethanol, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-8 mg/mlprotein1drop
235 %(w/v)ammonium sulfate1reservoir
30.1 unknownMES1reservoir
42 %(w/v)PEG6001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.94
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.95→38.31 Å / Num. all: 17694 / Num. obs: 17694 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 38.1
Reflection shellResolution: 1.95→2 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 8.6 / Num. unique all: 1209 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 184676
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 1209

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Processing

Software
NameVersionClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 1.95→20 Å / σ(F): 0 / Stereochemistry target values: PROTEIN dict.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 889 5 %RANDOM
Rwork0.216 ---
all-17362 --
obs-17362 100 %-
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1542 0 32 150 1724
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.005
X-RAY DIFFRACTIONp_angle_d0.017
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.216 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS

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