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- PDB-1n5j: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINAS... -

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Basic information

Entry
Database: PDB / ID: 1n5j
TitleCRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE DIPHOSPHATE (TDP) AND THYMIDINE TRIPHOSPHATE (TTP) AT PH 5.4 (1.85 A RESOLUTION)
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 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / THYMIDINE-5'-DIPHOSPHATE / Thymidylate kinase / Thymidylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.85 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 1.3Feb 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 / 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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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)23,7636
Polymers22,6631
Non-polymers1,1015
Water2,774154
1
A: THYMIDYLATE KINASE
hetero molecules

A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,52712
Polymers45,3252
Non-polymers2,20210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)76.248, 76.248, 135.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: x-y, -y, -z.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein THYMIDYLATE KINASE


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

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Non-polymers , 5 types, 159 molecules

#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-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#5: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.29 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 293 K / pH: 5.4
Details: Soaking in 30mM ATP, 40% PEG 2000, 10 mM ammonium sulphate, 0.1 M MES pH 5.4, 25 mM magnesium acetate, 2 mM mercaptoethanol, 3 mM EDTA, 1.5 mM DTT, VAPOR DIFFUSION, HANGING DROP + SOAKING

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2001
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→24.96 Å / Num. all: 19063 / Num. obs: 19063 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 16.6 Å2 / Rsym value: 0.055 / Net I/σ(I): 6
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2788 / Rsym value: 0.316 / % possible all: 94.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CNS1refinement
CCP4(SCALA)data scaling
CNS1phasing
RefinementMethod to determine structure: OTHER
Starting model: 1GSI

1gsi


Resolution: 1.85→24.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2014027.22 / Data cutoff high rms absF: 2014027.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The structure contains two conformations: conformation A corresponds to the TYD-bound state. Conformation B corresponds to the TTP-bound state.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 929 4.9 %RANDOM
Rwork0.215 ---
all0.215 19047 --
obs0.215 19047 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9412 Å2 / ksol: 0.358426 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å22.08 Å20 Å2
2--1.88 Å20 Å2
3----3.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.85→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 66 156 1768
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.041.5
X-RAY DIFFRACTIONc_mcangle_it1.52
X-RAY DIFFRACTIONc_scbond_it2.892
X-RAY DIFFRACTIONc_scangle_it3.662.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 152 4.8 %
Rwork0.254 3026 -
obs-3026 95.1 %
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_TTP_MOD.PARTMP_TDP_TTP_MOD.TOP

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