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Yorodumi- PDB-3dez: Crystal structure of Orotate phosphoribosyltransferase from Strep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dez | ||||||
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Title | Crystal structure of Orotate phosphoribosyltransferase from Streptococcus mutans | ||||||
Components | Orotate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / OROTATE PHOSPHORIBOSYLTRANSFERASE / Glycosyltransferase / Magnesium / Pyrimidine biosynthesis | ||||||
Function / homology | Function and homology information orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / nucleoside metabolic process / 'de novo' UMP biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Liu, C.P. / Gao, Z.Q. / Hou, H.F. / Li, L.F. / Su, X.D. / Dong, Y.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Structure of orotate phosphoribosyltransferase from the caries pathogen Streptococcus mutans Authors: Liu, C.P. / Xu, R. / Gao, Z.Q. / Xu, J.H. / Hou, H.F. / Li, L.Q. / She, Z. / Li, L.F. / Su, X.D. / Liu, P. / Dong, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dez.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dez.ent.gz | 69.4 KB | Display | PDB format |
PDBx/mmJSON format | 3dez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dez_validation.pdf.gz | 461.2 KB | Display | wwPDB validaton report |
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Full document | 3dez_full_validation.pdf.gz | 468.5 KB | Display | |
Data in XML | 3dez_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 3dez_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/3dez ftp://data.pdbj.org/pub/pdb/validation_reports/de/3dez | HTTPS FTP |
-Related structure data
Related structure data | 2aeeS 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: 26361.088 Da / Num. of mol.: 2 / Mutation: F92L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: pyrE / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q8DTV2, orotate phosphoribosyltransferase #2: Chemical | ChemComp-SO4 / #3: 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: 2.39 Å3/Da / Density % sol: 48.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 0.1M Tris hydrochloride, 2.3M Ammonium sulfate, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 19803 / % possible obs: 85.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12 % |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 10.9 % / Num. unique all: 2026 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AEE Resolution: 2.4→50 Å / σ(F): 1 / Stereochemistry target values: maximum likelihood
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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