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- PDB-5m4z: Crystal structure of the complex of T.spiralis thymidylate syntha... -

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Basic information

Entry
Database: PDB / ID: 5m4z
TitleCrystal structure of the complex of T.spiralis thymidylate synthase with N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate, crystallized in the presence of N(5,10)-methylenetetrahydrofolate
ComponentsThymidylate synthase
KeywordsTRANSFERASE / enzyme-inhibitor complex / high-resolution structure / anticancer target
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / mitochondrion / cytosol
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7K8 / Thymidylate synthase
Similarity search - Component
Biological speciesTrichinella spiralis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.179 Å
AuthorsWilk, P. / Maj, P. / Jarmula, A. / Dowiercial, A. / Rode, W.
CitationJournal: Int J Mol Sci / Year: 2021
Title: Molecular Mechanism of Thymidylate Synthase Inhibition by N 4 -Hydroxy-dCMP in View of Spectrophotometric and Crystallographic Studies.
Authors: Maj, P. / Jarmula, A. / Wilk, P. / Prokopowicz, M. / Rypniewski, W. / Zielinski, Z. / Dowiercial, A. / Bzowska, A. / Rode, W.
History
DepositionOct 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_radiation_wavelength
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,5929
Polymers74,4812
Non-polymers1,1117
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-23 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.290, 52.780, 63.920
Angle α, β, γ (deg.)72.470, 68.030, 61.150
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Thymidylate synthase


Mass: 37240.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichinella spiralis (invertebrata) / Gene: ts, Tsp_03568 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NDD3, thymidylate synthase
#2: Chemical ChemComp-7K8 / [(2~{R},3~{S},5~{R})-5-[(4~{E})-4-hydroxyimino-2-oxidanylidene-1,3-diazinan-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate


Mass: 325.212 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O8P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 0.1M NaF pH 7.1, 19% PEG 3350, 0.02% NaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.179→28.092 Å / Num. obs: 172936 / % possible obs: 97.41 % / Redundancy: 3.61 % / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rsym value: 0.04 / Net I/σ(I): 16.43
Reflection shellResolution: 1.179→1.21 Å / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4g9u

4g9u
PDB Unreleased entry


Resolution: 1.179→28.092 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 17.22
RfactorNum. reflection% reflection
Rfree0.1511 1816 1.05 %
Rwork0.1377 --
obs0.1379 172936 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.28 Å2 / Biso mean: 23.8067 Å2 / Biso min: 8.17 Å2
Refinement stepCycle: final / Resolution: 1.179→28.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4676 0 125 291 5092
Biso mean--31.51 32.66 -
Num. residues----573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084943
X-RAY DIFFRACTIONf_angle_d1.0866699
X-RAY DIFFRACTIONf_chiral_restr0.08703
X-RAY DIFFRACTIONf_plane_restr0.008864
X-RAY DIFFRACTIONf_dihedral_angle_d16.2621889
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1791-1.21090.28361270.2812118981202589
1.2109-1.24660.24741360.2396128621299895
1.2466-1.28680.24691400.211131681330897
1.2868-1.33280.19961390.1868131001323997
1.3328-1.38620.17611400.1703132171335798
1.3862-1.44930.1841400.1535131831332398
1.4493-1.52570.14511400.1325132141335498
1.5257-1.62120.15971420.1201133421348499
1.6212-1.74640.15131420.1163133811352399
1.7464-1.92210.10711420.1077134161355899
1.9221-2.20010.11391430.1097134611360499
2.2001-2.77160.14981430.12361343713580100
2.7716-28.10030.14791420.1424134411358399

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