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- PDB-4xsc: Complex structure of thymidylate synthase from varicella zoster v... -

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Basic information

Entry
Database: PDB / ID: 4xsc
TitleComplex structure of thymidylate synthase from varicella zoster virus with a phosphorylated BVDU
ComponentsThymidylate synthase
KeywordsTRANSFERASE / VZV / thymidylate synthase / herpesvirus
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation
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-BVP / Thymidylate synthase
Similarity search - Component
Biological speciesVaricella-zoster virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)145,68112
Polymers143,0754
Non-polymers2,6068
Water61334
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8406
Polymers71,5382
Non-polymers1,3034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-20 kcal/mol
Surface area21940 Å2
MethodPISA
2
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8406
Polymers71,5382
Non-polymers1,3034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-22 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.515, 149.515, 88.971
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 / Fragment: UNP residues 8-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Varicella-zoster virus (strain Oka vaccine)
Strain: Oka vaccine / Gene: ORF13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4JQW2, thymidylate synthase
#2: Chemical
ChemComp-BVP / (E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / BVDU-MP


Type: DNA linking / Mass: 413.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H14BrN2O8P
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8, 40% PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 49296 / % possible obs: 96.2 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 1.9 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XSE

4xse


Resolution: 2.901→29.706 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.45 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.235 2395 4.87 %
Rwork0.1955 --
obs0.1969 49207 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.901→29.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8853 0 138 34 9025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049223
X-RAY DIFFRACTIONf_angle_d0.80212506
X-RAY DIFFRACTIONf_dihedral_angle_d12.8973371
X-RAY DIFFRACTIONf_chiral_restr0.0311346
X-RAY DIFFRACTIONf_plane_restr0.0031587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9015-2.96060.34611700.24822704X-RAY DIFFRACTION94
2.9606-3.02470.30131350.23452762X-RAY DIFFRACTION95
3.0247-3.09480.32131400.24012772X-RAY DIFFRACTION95
3.0948-3.17190.31641640.22942724X-RAY DIFFRACTION94
3.1719-3.25720.28781520.22872703X-RAY DIFFRACTION95
3.2572-3.35260.29091200.21772776X-RAY DIFFRACTION96
3.3526-3.46020.26761520.21182733X-RAY DIFFRACTION95
3.4602-3.58320.26991820.19342688X-RAY DIFFRACTION94
3.5832-3.72570.24991220.19182789X-RAY DIFFRACTION96
3.7257-3.89390.22541640.19192704X-RAY DIFFRACTION94
3.8939-4.09740.20451700.17912716X-RAY DIFFRACTION94
4.0974-4.35140.18671400.17342749X-RAY DIFFRACTION95
4.3514-4.68310.19921280.16762770X-RAY DIFFRACTION96
4.6831-5.14640.1721040.17422783X-RAY DIFFRACTION96
5.1464-5.87290.1929900.1952781X-RAY DIFFRACTION97
5.8729-7.33240.20681360.19782749X-RAY DIFFRACTION95
7.3324-19.41690.17571260.17442756X-RAY DIFFRACTION95

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