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- PDB-3ca9: Evolution of chlorella virus dUTPase -

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Basic information

Entry
Database: PDB / ID: 3ca9
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.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase.
Authors: Homma, K. / Moriyama, H.
History
DepositionFeb 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,9056
Polymers35,0802
Non-polymers8254
Water34219
1
A: Deoxyuridine triphosphatase
hetero molecules

A: Deoxyuridine triphosphatase
hetero molecules

A: Deoxyuridine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8579
Polymers52,6203
Non-polymers1,2376
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area9450 Å2
ΔGint-37 kcal/mol
Surface area16200 Å2
MethodPISA
2
B: Deoxyuridine triphosphatase
hetero molecules

B: Deoxyuridine triphosphatase
hetero molecules

B: Deoxyuridine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8579
Polymers52,6203
Non-polymers1,2376
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9630 Å2
ΔGint-37.3 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.647, 105.647, 105.647
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-998-

MG

21B-999-

MG

31A-999-

HOH

41B-1001-

HOH

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Components

#1: Protein Deoxyuridine triphosphatase


Mass: 17539.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus IL3A
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.: 2 / Source method: obtained synthetically / Formula: C9H14N2O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG1450, 5mM magnesium chloride, 50mM sodium phosphate, 50mM sodium chloride, 1% glycerol, 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: Oct 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 8218 / Num. obs: 8200 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.58 / Num. unique all: 808 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30.5 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 3073620.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.307 865 10.7 %RANDOM
Rwork0.232 ---
all0.232 8099 --
obs0.232 8099 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.9855 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 3→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 50 19 1976
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_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.572
X-RAY DIFFRACTIONc_scangle_it2.52.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.464 141 10.7 %
Rwork0.395 1176 -
obs-1317 100 %

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