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- PDB-3c3i: Evolution of chlorella virus dUTPase -

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Basic information

Entry
Database: PDB / ID: 3c3i
TitleEvolution of chlorella virus dUTPase
ComponentsDeoxyuridine triphosphatase
KeywordsHYDROLASE / dUTPase Chlorella virus
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
DEOXYURIDINE-5'-DIPHOSPHATE / dUTP diphosphatase
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus IL3A
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYamanishi, M. / Homma, K. / Zhang, Y. / Etten, L.V.J. / Moriyama, H.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase.
Authors: Homma, K. / Moriyama, H.
#1: Journal: J.Virol. / Year: 2005
Title: Chlorella virus-encoded deoxyuridine triphosphatases exhibit different temperature optima.
Authors: Zhang, Y. / Moriyama, H. / Homma, K. / Van Etten, J.L.
History
DepositionJan 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyuridine triphosphatase
B: Deoxyuridine triphosphatase
C: Deoxyuridine triphosphatase
D: Deoxyuridine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,90110
Polymers59,3004
Non-polymers1,6016
Water36020
1
A: Deoxyuridine triphosphatase
hetero molecules

A: Deoxyuridine triphosphatase
hetero molecules

A: Deoxyuridine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7129
Polymers44,4753
Non-polymers1,2376
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area10310 Å2
MethodPISA
2
B: Deoxyuridine triphosphatase
C: Deoxyuridine triphosphatase
D: Deoxyuridine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6647
Polymers44,4753
Non-polymers1,1894
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.069, 132.069, 53.451
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-998-

MG

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Components

#1: Protein
Deoxyuridine triphosphatase


Mass: 14824.925 Da / Num. of mol.: 4 / Mutation: E81S, T84R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus IL3A
Strain: MU-22 / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-pLys / References: UniProt: Q5I3E5, dUTP diphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-DUD / DEOXYURIDINE-5'-DIPHOSPHATE


Mass: 388.162 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG1500, 50mM sodium phosphate, 50mM sodium chloride, 2mM dUDP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19947 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.332 / % possible all: 91.1

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Processing

Software
NameVersionClassification
CNS1.2refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→33.61 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 413776.68 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1059 9.8 %RANDOM
Rwork0.195 ---
obs0.195 10768 99 %-
all-21086 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.8395 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.49 Å20 Å20 Å2
2---7.49 Å20 Å2
3---14.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 3→33.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3935 0 98 20 4053
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.991.5
X-RAY DIFFRACTIONc_mcangle_it1.722
X-RAY DIFFRACTIONc_scbond_it1.392
X-RAY DIFFRACTIONc_scangle_it2.222.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 157 9 %
Rwork0.256 1578 -
obs--97.6 %

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