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- PDB-7cc8: Crystal structure of White Spot Syndrome Virus Thymidylate Syntha... -

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Basic information

Entry
Database: PDB / ID: 7cc8
TitleCrystal structure of White Spot Syndrome Virus Thymidylate Synthase - Apo form
ComponentsThymidylate Synthase
KeywordsTRANSFERASE / Thymidylate Synthase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / methylation
Similarity search - Function
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
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Thymidylate synthase
Similarity search - Component
Biological speciesWhite spot syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKumar, S. / Panchal, N.V. / Shaikh, N. / Vasudevan, D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR23375/AAQ/3/849/2017 India
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Structure analysis of thymidylate synthase from white spot syndrome virus reveals WSSV-specific structural elements.
Authors: Panchal, V. / Kumar, S. / Hossain, S.N. / Vasudevan, D.
History
DepositionJun 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 29, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,41411
Polymers68,3872
Non-polymers1,0279
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-109 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.801, 91.801, 233.578
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Thymidylate Synthase / Wsv067


Mass: 34193.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) White spot syndrome virus (isolate Shrimp/China/Tongan/1996)
Strain: isolate Shrimp/China/Tongan/1996 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q77J90
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.6 Å3/Da / Density % sol: 65.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM ammonium sulfate, 100 mM Bis-Tris (pH 6.5), 23% PEG3350, 4% Pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97242 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.3→43.41 Å / Num. obs: 42497 / % possible obs: 98.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 38.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4356 / CC1/2: 0.807 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X5D

5x5d


Resolution: 2.3→43.41 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.209 2277 -
Rwork0.185 --
obs-42497 98.9 %
Displacement parametersBiso max: 127.32 Å2 / Biso mean: 34.3783 Å2 / Biso min: 19.97 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4629 0 57 164 4850
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.209 --
Rwork0.185 --
obs-4356 99.8 %

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