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- PDB-6ljj: Swine dUTPase in complex with alpha,beta-iminodUTP and magnesium ion -

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Basic information

Entry
Database: PDB / ID: 6ljj
TitleSwine dUTPase in complex with alpha,beta-iminodUTP and magnesium ion
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial isoform 1
KeywordsHYDROLASE / swine dUTPase / sDUT / dUTPase
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 / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsLiang, R. / Peng, G.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31722056 China
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural comparisons of host and African swine fever virus dUTPases reveal new clues for inhibitor development.
Authors: Liang, R. / Wang, G. / Zhang, D. / Ye, G. / Li, M. / Shi, Y. / Shi, J. / Chen, H. / Peng, G.
History
DepositionDec 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7633
Polymers17,2711
Non-polymers4912
Water2,846158
1
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial isoform 1
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial isoform 1
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2889
Polymers51,8143
Non-polymers1,4746
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation59_555y,-z,-x1
crystal symmetry operation80_555-z,x,-y1
Buried area16920 Å2
ΔGint-103 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.386, 162.386, 162.386
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

21A-454-

HOH

31A-510-

HOH

41A-514-

HOH

51A-530-

HOH

61A-531-

HOH

71A-552-

HOH

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Components

#1: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial isoform 1


Mass: 17271.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A480PG39
#2: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: 0.2 M Magnesium Formate pH 5.9, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.885→50.01 Å / Num. obs: 19159 / % possible obs: 99.5 % / Redundancy: 10 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.012 / Rrim(I) all: 0.098 / Χ2: 0.946 / Net I/σ(I): 6
Reflection shellResolution: 1.885→1.91 Å / Redundancy: 7.78 % / Rmerge(I) obs: 0.788 / Num. unique obs: 770 / CC1/2: 0.977 / CC star: 0.994 / Rpim(I) all: 0.092 / Rrim(I) all: 0.788 / Χ2: 1.222 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LIW

6liw
PDB Unreleased entry


Resolution: 1.89→27.46 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.888 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 735 5 %RANDOM
Rwork0.1966 ---
obs0.1983 13847 94.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.75 Å2 / Biso mean: 22.972 Å2 / Biso min: 12.24 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.89→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1135 0 29 158 1322
Biso mean--16.28 35.2 -
Num. residues----150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131191
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171039
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.681617
X-RAY DIFFRACTIONr_angle_other_deg1.4471.5942388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5285149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56120.63563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1915170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.308159
X-RAY DIFFRACTIONr_chiral_restr0.080.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02273
LS refinement shellResolution: 1.89→1.934 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.599 25 -
Rwork0.587 420 -
obs--40.05 %

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