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- PDB-5nrq: Mtb TMK crystal structure in complex with compound 33 -

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Basic information

Entry
Database: PDB / ID: 5nrq
TitleMtb TMK crystal structure in complex with compound 33
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Thymidylate kinase / Nucleotide Binding / inhibitor
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 / 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
Chem-ZUI / Thymidylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMerceron, R. / Song, L. / Munier-Lehmann, H. / Van Calenbergh, S. / Savvides, S.
CitationJournal: To Be Published
Title: Mtb TMK crystal structure in complex with compound LS3112
Authors: Merceron, R. / Song, L. / Munier-Lehmann, H. / Van Calenbergh, S. / Savvides, S.
History
DepositionApr 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)46,3218
Polymers45,3252
Non-polymers9966
Water2,198122
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-44 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.850, 73.850, 72.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Thymidylate kinase / Thymidine monophosphate kinase / dTMP kinase / TMPK


Mass: 22662.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: tmk, Rv3247c / Production host: Escherichia coli (E. coli) / Strain (production host): BLi5 / References: UniProt: P9WKE1, dTMP kinase
#2: Chemical ChemComp-ZUI / 1-[1-[[5-(3-chloranylphenoxy)pyridin-3-yl]methyl]piperidin-4-yl]-5-methyl-pyrimidine-2,4-dione


Mass: 426.896 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23ClN4O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 51.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 4.3 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 25255 / % possible obs: 98 % / Redundancy: 3.65 % / Biso Wilson estimate: 48.9 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.074 / Rsym value: 0.064 / Net I/σ(I): 12.03
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.45 % / Mean I/σ(I) obs: 1.26 / CC1/2: 0.432 / Rrim(I) all: 1.071 / Rsym value: 0.908 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UNR

4unr


Resolution: 2.1→36.925 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 1263 5 %Random selection
Rwork0.1784 ---
obs0.1801 25255 98.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→36.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 64 122 2858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072788
X-RAY DIFFRACTIONf_angle_d0.8463804
X-RAY DIFFRACTIONf_dihedral_angle_d14.9871626
X-RAY DIFFRACTIONf_chiral_restr0.052434
X-RAY DIFFRACTIONf_plane_restr0.005532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.18420.33181410.30182673X-RAY DIFFRACTION99
2.1842-2.28360.28031410.25732693X-RAY DIFFRACTION99
2.2836-2.4040.27561420.23942697X-RAY DIFFRACTION99
2.404-2.55460.25961410.22322666X-RAY DIFFRACTION99
2.5546-2.75180.27171420.22132699X-RAY DIFFRACTION99
2.7518-3.02860.25051390.212649X-RAY DIFFRACTION98
3.0286-3.46650.19041410.17952670X-RAY DIFFRACTION98
3.4665-4.36630.17231380.14142632X-RAY DIFFRACTION97
4.3663-36.93070.17811380.14272613X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.12440.29490.60023.1135-1.76432.7207-0.0003-0.0611-0.5231-0.1438-0.0587-0.2570.0939-0.02980.05770.33090.00420.05290.2677-0.01220.3231-17.856713.429-13.4919
21.3867-0.4118-0.12967.8153-3.63393.8529-0.1371-0.081-0.1497-0.3365-0.1802-0.59860.12680.0510.27450.42920.0301-0.0620.33970.05860.4093-21.815-10.466713.5837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 209)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 209)

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