+Open data
-Basic information
Entry | Database: PDB / ID: 7bpd | ||||||
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Title | Crystal structural analysis of Swine dUTPase | ||||||
Components | Deoxyuridine triphosphataseDUTP diphosphatase | ||||||
Keywords | HYDROLASE / SWINE / dUTPASE / sDUT | ||||||
Function / homology | Function and homology information dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Liang, R. / Peng, G.Q. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structural analysis of swine dUTPase Authors: Liang, R. / Peng, G.Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bpd.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bpd.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 7bpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/7bpd ftp://data.pdbj.org/pub/pdb/validation_reports/bp/7bpd | HTTPS FTP |
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-Related structure data
Related structure data | 2hquS S: Starting model for refinement |
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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: 18537.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: DUT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4X1SHL3 #2: Water | ChemComp-HOH / | |
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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: 1.99 Å3/Da / Density % sol: 38.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 200mM NaI, 20% (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: 0.97835 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97835 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→51.9 Å / Num. obs: 35796 / % possible obs: 83 % / Redundancy: 5.7 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Χ2: 0.968 / Net I/σ(I): 23.67 |
Reflection shell | Resolution: 2.04→2.08 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2 / Num. unique obs: 1301 / CC1/2: 0.972 / CC star: 0.993 / Rpim(I) all: 0.378 / Rrim(I) all: 0.968 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HQU Resolution: 2.04→46.62 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.063 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.4 Å2 / Biso mean: 38.493 Å2 / Biso min: 0.94 Å2
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Refinement step | Cycle: final / Resolution: 2.04→46.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.083 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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