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Yorodumi- PDB-6lj3: full length ASFV dUTPase in complex with alpha,beta-iminodUTP and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lj3 | ||||||
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Title | full length ASFV dUTPase in complex with alpha,beta-iminodUTP and magnesium ion | ||||||
Components | E165R | ||||||
Keywords | VIRAL PROTEIN / ASFV / dUTPase / aDUT | ||||||
Function / homology | Function and homology information dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / virion component / host cell cytoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | African swine fever virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Liang, R. / Peng, G.Q. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lj3.cif.gz | 114.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lj3.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 6lj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/6lj3 ftp://data.pdbj.org/pub/pdb/validation_reports/lj/6lj3 | HTTPS FTP |
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-Related structure data
Related structure data | 6lisSC 6ljjC 6ljoC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18285.447 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African swine fever virus Gene: E165R CDS, E165R, ASFV-Georgia_4-154, ASFV_Kyiv_2016_131_00207 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X0SE53, UniProt: Q65199*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M sodium citrate, 0.1 m, 24% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→59.19 Å / Num. obs: 34696 / % possible obs: 85 % / Redundancy: 11.3 % / CC1/2: 1 / Net I/σ(I): 1.86 |
Reflection shell | Resolution: 1.96→2.07 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.83 / Num. unique obs: 1166 / CC1/2: 0.698 / CC star: 0.907 / Rpim(I) all: 0.322 / Rrim(I) all: 0.965 / Χ2: 0.941 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LIS Resolution: 2→34.24 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.099 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.194 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.51 Å2 / Biso mean: 23.855 Å2 / Biso min: 7.21 Å2
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Refinement step | Cycle: final / Resolution: 2→34.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.961→2.012 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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