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- PDB-1n5l: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINAS... -

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Basic information

Entry
Database: PDB / ID: 1n5l
TitleCRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE CRYSTALLIZED IN SODIUM MALONATE, AFTER CATALYSIS IN THE CRYSTAL (2.3 A RESOLUTION)
ComponentsTHYMIDYLATE KINASE
KeywordsTRANSFERASE / TRANSFERASE (ATP:TMP PHOSPHOTRANSFERASE) / KINASE
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 / DIPHOSPHATE / THYMIDINE-5'-PHOSPHATE / THYMIDINE-5'-DIPHOSPHATE / Thymidylate kinase / Thymidylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsFioravanti, E. / Haouz, A. / Ursby, T. / Munier-Lehmann, H. / Delarue, M. / Bourgeois, D.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Mycobacterium tuberculosis Thymidylate Kinase: Structural Studies of Intermediates along the Reaction Pathway
Authors: Fioravanti, E. / Haouz, A. / Ursby, T. / Munier-Lehmann, H. / Delarue, M. / Bourgeois, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Cryo-Photolysis of Caged Compounds: A Technique for Trapping Intermediate States in Protein Crystals
Authors: Ursby, T. / Weik, M. / Fioravanti, E. / Delarue, M. / Goeldner, M. / Bourgeois, D.
#2: 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.
#3: 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.
History
DepositionNov 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN HOH molecules 140 and 141 were both named 140 in the paper because they occupy the same ...HETEROGEN HOH molecules 140 and 141 were both named 140 in the paper because they occupy the same site in the 2 monomers (A and B), in order to make an easier comparison of the active sites.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,3668
Polymers45,3252
Non-polymers1,0416
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.454, 64.454, 195.899
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe asymmetric unit contains the functional dimer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein THYMIDYLATE KINASE /


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

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Non-polymers , 6 types, 211 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#6: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.64 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 293 K
Method: vapor diffusion, hanging drop, streak seeding, soaking
pH: 6
Details: 1.4 M sodium malonate, 2% PEG 2000, 0.1 M MES pH 6.0, 2 mM b-mercaptoethanol, 25 mM magnesium acetate, soaking in 30 mM ATP, VAPOR DIFFUSION, HANGING DROP, STREAK SEEDING, SOAKING

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.936 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2001
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 2.3→19.76 Å / Num. all: 21648 / Num. obs: 21648 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 41 Å2 / Rsym value: 0.107 / Net I/σ(I): 4.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 2977 / Rsym value: 0.381 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNS1refinement
CCP4(SCALA)data scaling
CNS1phasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1N5K

1n5k


Resolution: 2.3→19.76 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1848944.31 / Data cutoff high rms absF: 1848944.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Monomer A contains the apo-structure. Monomer B contains the TDP-Mg++-ADP complex.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1054 4.9 %RANDOM
Rwork0.236 ---
all0.238 21577 --
obs0.236 21577 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.1841 Å2 / ksol: 0.34923 e/Å3
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.08 Å24.7 Å20 Å2
2--6.08 Å20 Å2
3----12.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 63 205 3173
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_mcbond_it3.411.5
X-RAY DIFFRACTIONc_mcangle_it5.312
X-RAY DIFFRACTIONc_scbond_it5.062
X-RAY DIFFRACTIONc_scangle_it6.322.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 165 4.7 %
Rwork0.247 3345 -
obs-3345 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4TMP+TDP+ACT+DPO.PARTMP+TDP+ACT+DPO.TOP

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