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Yorodumi- PDB-2oge: x-ray structure of S. venezuelae DesV in its internal aldimine form -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oge | ||||||
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Title | x-ray structure of S. venezuelae DesV in its internal aldimine form | ||||||
Components | Transaminase | ||||||
Keywords | TRANSFERASE / PLP-dependent enzyme / desosamine / transaminase / deoxysugars / macrolide antibiotics | ||||||
Function / homology | Function and homology information dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose transaminase / polysaccharide biosynthetic process / macrolide biosynthetic process / transaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Streptomyces venezuelae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Holden, H.M. / Burgie, E.S. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Molecular architecture of DesV from Streptomyces venezuelae: A PLP-dependent transaminase involved in the biosynthesis of the unusual sugar desosamine. Authors: Burgie, E.S. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oge.cif.gz | 328.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oge.ent.gz | 258.7 KB | Display | PDB format |
PDBx/mmJSON format | 2oge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/2oge ftp://data.pdbj.org/pub/pdb/validation_reports/og/2oge | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Des V is a homodimer. The asymmetric unit comprises two dimers. Subunits A and B make up dimer one, and subunits C and D make up the second dimer. |
-Components
#1: Protein | Mass: 43822.992 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: desV / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q9ZGH4 #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: 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: 2.3 Å3/Da / Density % sol: 46.44 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 6 Details: 12% PEG 3400, 1% ethylene glycol, 50 mM MES, 50 mM glutamate, 75 mM NaCl, pH 6.0, batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: BRUKER PROTEUM / Detector: CCD / Date: Feb 8, 2006 / Details: Montel |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30.5 Å / Num. all: 92487 / Num. obs: 92487 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.077 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.05→2.15 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 11559 / Rsym value: 0.286 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→30.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Displacement parameters | Biso mean: 24.776 Å2 | ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→30.5 Å
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