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- PDB-5nrn: Mtb TMK crystal structure in complex with compound 3 -

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Basic information

Entry
Database: PDB / ID: 5nrn
TitleMtb TMK crystal structure in complex with compound 3
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-95W / Thymidylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 LS3080
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

Downloads & links

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Assembly

Deposited unit
A: Thymidylate kinase
B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,35811
Polymers45,3252
Non-polymers1,0339
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-70 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.230, 130.230, 120.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21B-434-

HOH

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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 H37Rv (bacteria)
Gene: tmk, Rv3247c / Production host: Escherichia coli (E. coli) / Variant (production host): BLi5 / References: UniProt: P9WKE1, dTMP kinase
#2: Chemical ChemComp-95W / 5-methyl-1-[1-[(6-phenoxypyridin-2-yl)methyl]piperidin-4-yl]pyrimidine-2,4-dione


Mass: 392.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24N4O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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

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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 52835 / % possible obs: 99.8 % / Redundancy: 6.55 % / Biso Wilson estimate: 52.7 Å2 / CC1/2: 1 / Rrim(I) all: 0.057 / Rsym value: 0.053 / Net I/σ(I): 24.45
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.66 % / Mean I/σ(I) obs: 1.69 / Num. unique obs: 3792 / CC1/2: 0.76 / Rrim(I) all: 1.399 / Rsym value: 1.29 / % possible all: 98.6

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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: 2.2→46.043 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.14
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 2640 5 %Random selection
Rwork0.1721 ---
obs0.1735 52822 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 65 280 3256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063077
X-RAY DIFFRACTIONf_angle_d0.744189
X-RAY DIFFRACTIONf_dihedral_angle_d19.7041829
X-RAY DIFFRACTIONf_chiral_restr0.045462
X-RAY DIFFRACTIONf_plane_restr0.005595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.24010.29321350.27312563X-RAY DIFFRACTION98
2.2401-2.28320.26221370.24922608X-RAY DIFFRACTION100
2.2832-2.32980.2661360.23272611X-RAY DIFFRACTION100
2.3298-2.38050.25981360.21582579X-RAY DIFFRACTION100
2.3805-2.43580.24241370.20792605X-RAY DIFFRACTION100
2.4358-2.49680.23141390.20122630X-RAY DIFFRACTION100
2.4968-2.56430.28251370.2112603X-RAY DIFFRACTION100
2.5643-2.63970.24731370.21322608X-RAY DIFFRACTION100
2.6397-2.72490.2781380.21512640X-RAY DIFFRACTION100
2.7249-2.82230.23971370.22122605X-RAY DIFFRACTION100
2.8223-2.93530.2331380.21222624X-RAY DIFFRACTION100
2.9353-3.06880.20941400.19192649X-RAY DIFFRACTION100
3.0688-3.23060.2081390.18472639X-RAY DIFFRACTION100
3.2306-3.43290.1751390.15322658X-RAY DIFFRACTION100
3.4329-3.69790.16931400.14172643X-RAY DIFFRACTION100
3.6979-4.06980.16841400.13482662X-RAY DIFFRACTION100
4.0698-4.65820.14231420.1252694X-RAY DIFFRACTION100
4.6582-5.8670.17331420.15682709X-RAY DIFFRACTION100
5.867-46.05330.21731510.1852852X-RAY DIFFRACTION99
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)
13.8878-0.7650.94623.35970.48552.02080.04710.35-0.0252-0.2452-0.17320.3516-0.1023-0.15370.12380.3154-0.0201-0.02060.4334-0.0580.3502-44.636-26.4421-18.3207
23.25-0.24340.62811.63950.3531.87970.09430.1708-0.042-0.0259-0.0614-0.08230.11350.2169-0.03580.3269-0.02340.06850.4324-0.03330.351-11.2135-36.2755-5.334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 211)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 211)

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