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- PDB-1w2h: Crystal Structure Of Mycobacterium Tuberculosis Thymidylate Kinas... -

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Basic information

Entry
Database: PDB / ID: 1w2h
TitleCrystal Structure Of Mycobacterium Tuberculosis Thymidylate Kinase Complexed With Azidothymidine Monophosphate (AZT-MP) (2.0 A Resolution)
ComponentsTHYMIDYLATE KINASE TMK
KeywordsTRANSFERASE / MYCOBACTERIUM TUBERCULOSIS / THYMIDYLATE KINASE / AZT / INHIBITION MECHANISM
Function / homology
Function and homology information


TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / GTP binding / magnesium ion binding / protein homodimerization activity ...TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE / Thymidylate kinase / Thymidylate kinase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFioravanti, E. / Adam, V. / Munier-Lehmann, H. / Bourgeois, D.
CitationJournal: Biochemistry / Year: 2005
Title: The crystal structure of Mycobacterium tuberculosis thymidylate kinase in complex with 3'-azidodeoxythymidine monophosphate suggests a mechanism for competitive inhibition.
Authors: Fioravanti, E. / Adam, V. / Munier-Lehmann, H. / Bourgeois, D.
History
DepositionJul 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2005Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 19, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation / struct_conn
Item: _atom_site.label_alt_id / _citation.page_last ..._atom_site.label_alt_id / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THYMIDYLATE KINASE TMK
B: THYMIDYLATE KINASE TMK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5448
Polymers45,3252
Non-polymers1,2196
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.521, 64.521, 195.366
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein THYMIDYLATE KINASE TMK / DTMP KINASE / THYMIDYLIC ACID KINASE / TMPK


Mass: 22662.525 Da / Num. of mol.: 2
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-ATM / 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.59 Å3/Da / Density % sol: 52.51 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: May 12, 2003 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→42.26 Å / Num. obs: 30873 / % possible obs: 92.2 % / Observed criterion σ(I): 1.7 / Redundancy: 4.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.6
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.42 / % possible all: 92.2

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N5K

1n5k


Resolution: 2→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED REGIONS WERE CUT FROM THE MODEL AND SOME RESIDUES WERE MODELED IN ALTERNATE CONFORMATIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1519 5 %RANDOM
Rwork0.259 ---
obs0.259 30023 89.1 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.671 Å2-3.098 Å20 Å2
2---8.671 Å20 Å2
3---17.342 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati sigma a0.32 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 77 210 3137
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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