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- PDB-4xse: Complex structure of thymidylate synthase from varicella zoster virus -

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Basic information

Entry
Database: PDB / ID: 4xse
TitleComplex structure of thymidylate synthase from varicella zoster virus
ComponentsThymidylate synthase
KeywordsVIRAL PROTEIN / thymidylate synthase / herpesvirus / varicella zoster virus / vzv
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / dihydrofolate reductase activity / methylation / cytosol
Similarity search - Function
Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Thymidylate synthase
Similarity search - Component
Biological speciesVaricella-zoster virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHew, K.
CitationJournal: Plos One / Year: 2015
Title: Structure of the Varicella Zoster Virus Thymidylate Synthase Establishes Functional and Structural Similarities as the Human Enzyme and Potentiates Itself as a Target of Brivudine.
Authors: Hew, K. / Dahlroth, S.L. / Veerappan, S. / Pan, L.X. / Cornvik, T. / Nordlund, P.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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
C: Thymidylate synthase
B: Thymidylate synthase
D: Thymidylate synthase
A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,4558
Polymers143,0754
Non-polymers3804
Water0
1
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7284
Polymers71,5382
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-30 kcal/mol
Surface area23610 Å2
MethodPISA
2
B: Thymidylate synthase
A: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7284
Polymers71,5382
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-29 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.379, 153.379, 89.180
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 synthase / / TSase


Mass: 35768.848 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Varicella-zoster virus (strain Oka vaccine)
Gene: ORF13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4JQW2, thymidylate synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.23 Å3/Da / Density % sol: 70.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12% ethylene glycol, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→29.8 Å / Num. obs: 42243 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.5
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.475 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HZW

1hzw


Resolution: 3.1→29.727 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 35.83 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.268 1985 4.7 %
Rwork0.2383 --
obs0.2393 42223 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→29.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9060 0 20 0 9080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019330
X-RAY DIFFRACTIONf_angle_d1.44712655
X-RAY DIFFRACTIONf_dihedral_angle_d15.0583429
X-RAY DIFFRACTIONf_chiral_restr0.0561350
X-RAY DIFFRACTIONf_plane_restr0.0081624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1009-3.17830.32181280.29292866X-RAY DIFFRACTION93
3.1783-3.26420.3896850.27132852X-RAY DIFFRACTION95
3.2642-3.36010.341690.27032795X-RAY DIFFRACTION93
3.3601-3.46830.31421300.26112871X-RAY DIFFRACTION94
3.4683-3.59210.27531510.24472865X-RAY DIFFRACTION94
3.5921-3.73560.29911530.24882866X-RAY DIFFRACTION94
3.7356-3.90520.30451620.24182838X-RAY DIFFRACTION94
3.9052-4.11050.27851430.2372901X-RAY DIFFRACTION95
4.1105-4.36720.21391300.21972904X-RAY DIFFRACTION96
4.3672-4.7030.22991960.21692845X-RAY DIFFRACTION94
4.703-5.17370.2641140.21752908X-RAY DIFFRACTION96
5.1737-5.91640.25271600.23362905X-RAY DIFFRACTION95
5.9164-7.43190.27231280.24862889X-RAY DIFFRACTION96
7.4319-28.40220.21331190.2162911X-RAY DIFFRACTION96

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