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

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Basic information

Entry
Database: PDB / ID: 4xsd
TitleComplex structure of thymidylate synthase from varicella zoster virus with a dUMP
ComponentsThymidylate synthase
KeywordsVIRAL PROTEIN / VZV / thymidylate synthase / herpesvirus
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
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Thymidylate synthase
Similarity search - Component
Biological speciesVaricella-zoster virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
A: Thymidylate synthase
B: Thymidylate synthase
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,3088
Polymers143,0754
Non-polymers1,2334
Water1629
1
A: Thymidylate synthase
B: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1544
Polymers71,5382
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-30 kcal/mol
Surface area21840 Å2
MethodPISA
2
C: Thymidylate synthase
D: Thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1544
Polymers71,5382
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-31 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.170, 150.170, 89.160
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)
Strain: Oka vaccine / Gene: ORF13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4JQW2, thymidylate synthase
#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.06 Å3/Da / Density % sol: 69.68 %
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 315r / Detector: CCD / Date: Jul 5, 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: 49612 / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.9 / % possible all: 99.9

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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: 2.9→29.836 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.93 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2803 2419 5.02 %
Rwork0.2402 --
obs0.2418 48187 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→29.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8761 0 80 9 8850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049074
X-RAY DIFFRACTIONf_angle_d0.88212322
X-RAY DIFFRACTIONf_dihedral_angle_d14.2973306
X-RAY DIFFRACTIONf_chiral_restr0.0321332
X-RAY DIFFRACTIONf_plane_restr0.0041565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9015-2.96050.31861720.29642569X-RAY DIFFRACTION88
2.9605-3.02460.31851280.29342592X-RAY DIFFRACTION90
3.0246-3.09470.36011230.29182601X-RAY DIFFRACTION89
3.0947-3.17180.31491470.28962638X-RAY DIFFRACTION90
3.1718-3.25720.31881650.2752614X-RAY DIFFRACTION89
3.2572-3.35260.29091200.26142711X-RAY DIFFRACTION93
3.3526-3.46020.25881250.25992680X-RAY DIFFRACTION93
3.4602-3.58310.32331900.24912715X-RAY DIFFRACTION92
3.5831-3.72570.28761300.24282758X-RAY DIFFRACTION95
3.7257-3.89390.31021560.23992743X-RAY DIFFRACTION93
3.8939-4.09740.27311710.23282684X-RAY DIFFRACTION93
4.0974-4.35150.24751460.21482732X-RAY DIFFRACTION94
4.3515-4.68320.24941220.20992763X-RAY DIFFRACTION94
4.6832-5.14660.25271080.2142727X-RAY DIFFRACTION94
5.1466-5.87340.2482810.24292727X-RAY DIFFRACTION94
5.8734-7.33370.28571300.24732603X-RAY DIFFRACTION89
7.3337-19.49370.23381280.21432797X-RAY DIFFRACTION96

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