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- PDB-3so2: Chlorella dUTPase -

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Basic information

Entry
Database: PDB / ID: 3so2
TitleChlorella dUTPase
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / Deoxyuridine triphosphatase / dUTPase / chlorella / cancer marker
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'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesChlorella variabilis (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6428 Å
AuthorsBadalucco, L. / Poudel, I. / Natarajan, c. / Yamanishi, M. / Moriyama, H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization of Chlorella deoxyuridine triphosphatase.
Authors: Badalucco, L. / Poudel, I. / Yamanishi, M. / Natarajan, C. / Moriyama, H.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)15,3801
Polymers15,3801
Non-polymers00
Water2,198122
1
A: Putative uncharacterized protein

A: Putative uncharacterized protein

A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)46,1413
Polymers46,1413
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11260 Å2
ΔGint-40 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.910, 66.910, 93.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-149-

HOH

21A-161-

HOH

31A-162-

HOH

41A-181-

HOH

51A-210-

HOH

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Components

#1: Protein Putative uncharacterized protein


Mass: 15380.247 Da / Num. of mol.: 1 / Fragment: UNP Residues 28-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorella variabilis (plant) / Gene: CHLNCDRAFT_27939 / Plasmid details: Codon optimized / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E1ZRW6, dUTP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 2.2 M ammonium sulfate, 1 mM magnesium chloride, 50 mM TRIS buffer pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 118 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→27.678 Å / Num. all: 19105 / Num. obs: 18497 / % possible obs: 96.8 % / Observed criterion σ(F): 2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.refine: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-3000data scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EHW

3ehw


Resolution: 1.6428→27.678 Å / SU ML: 0.5 / σ(F): 0.09 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 1846 9.98 %RANDOM
Rwork0.2497 ---
obs0.2512 18497 97.08 %-
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.39 Å2 / ksol: 0.452 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2012 Å2-0 Å20 Å2
2---0.2012 Å2-0 Å2
3---0.4025 Å2
Refinement stepCycle: LAST / Resolution: 1.6428→27.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 0 0 122 1143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121039
X-RAY DIFFRACTIONf_angle_d1.4451411
X-RAY DIFFRACTIONf_dihedral_angle_d16.455380
X-RAY DIFFRACTIONf_chiral_restr0.087162
X-RAY DIFFRACTIONf_plane_restr0.008190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6428-1.68720.47941320.4271186X-RAY DIFFRACTION92
1.6872-1.73680.41831460.33221298X-RAY DIFFRACTION97
1.7368-1.79290.34331420.29461291X-RAY DIFFRACTION98
1.7929-1.85690.30891470.25561294X-RAY DIFFRACTION98
1.8569-1.93130.31121350.25381271X-RAY DIFFRACTION95
1.9313-2.01910.28521450.24471284X-RAY DIFFRACTION99
2.0191-2.12560.30981440.24451326X-RAY DIFFRACTION100
2.1256-2.25870.2851260.24821145X-RAY DIFFRACTION86
2.2587-2.4330.25561450.23351269X-RAY DIFFRACTION97
2.433-2.67760.24271460.23061334X-RAY DIFFRACTION100
2.6776-3.06470.24531500.24321316X-RAY DIFFRACTION100
3.0647-3.85950.25171460.23861316X-RAY DIFFRACTION100
3.8595-27.6820.22541420.25151321X-RAY DIFFRACTION100

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