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Yorodumi- PDB-3opx: Crystal structure of pyrimidine 5 -nucleotidase SDT1 from Sacchar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3opx | ||||||
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Title | Crystal structure of pyrimidine 5 -nucleotidase SDT1 from Saccharomyces cerevisiae complexed with uridine 5'-monophosphate | ||||||
Components | Protein SSM1 | ||||||
Keywords | HYDROLASE / Rossmann fold / nucleotidase / U5P Binding / magnesium Binding | ||||||
Function / homology | Function and homology information nucleotidase activity / pyrimidine nucleobase metabolic process / nucleotide catabolic process Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Teng, M.K. / Niu, L.W. / Shi, N. | ||||||
Citation | Journal: To be published Title: Crystal structure of pyrimidine 5 -nucleotidase SDT1 from Saccharomyces cerevisiae complexed with uridine 5'-monophosphate Authors: Shi, N. / Teng, M.K. / Niu, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3opx.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3opx.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 3opx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3opx_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3opx_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3opx_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3opx_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/3opx ftp://data.pdbj.org/pub/pdb/validation_reports/op/3opx | HTTPS FTP |
-Related structure data
Related structure data | 3onnS 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: 30190.705 Da / Num. of mol.: 1 / Fragment: UNP residues 26-280 / Mutation: D36A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SSM1, SDT1, YGL224C / Production host: Escherichia coli (E. coli) / References: UniProt: P53078 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-U5P / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.19 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG4000, 0.1M Tris-HCl buffer, pH 8.5, 0.2M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 287.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9194 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 26, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9194 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35 Å / Num. all: 30175 / Num. obs: 30137 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 39.6 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 5.4 / Num. unique all: 1471 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ONN Resolution: 1.7→29.201 Å / SU ML: 0.23 / σ(F): 0.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.192 Å2 / ksol: 0.366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→29.201 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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