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Yorodumi- PDB-2oga: X-ray crystal structure of S. venezuelae DesV in complex with ket... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oga | ||||||
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Title | X-ray crystal structure of S. venezuelae DesV in complex with ketimine intermediate | ||||||
Components | Transaminase | ||||||
Keywords | HYDROLASE / PLP-dependent enzyme / desosamine / transaminase / deoxysugars / antibiotics | ||||||
Function / homology | Function and homology information dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose transaminase / macrolide biosynthetic process / polysaccharide 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 | 2oga.cif.gz | 319.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oga.ent.gz | 254.4 KB | Display | PDB format |
PDBx/mmJSON format | 2oga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oga_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 2oga_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 2oga_validation.xml.gz | 74.1 KB | Display | |
Data in CIF | 2oga_validation.cif.gz | 103.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/2oga ftp://data.pdbj.org/pub/pdb/validation_reports/og/2oga | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | homodimer. asymmetric unit is comprised of two homodimers, A+B, and C+D |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 43594.875 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 |
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-Non-polymers , 5 types, 1025 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PGU / #6: 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: 2.15 Å3/Da / Density % sol: 42.9 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 6 Details: 12% PEG 3400, 1% ethylene glycol, 50 mM MES, 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 6, 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→36 Å / Num. all: 80130 / Num. obs: 80130 / % possible obs: 84.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.072 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.05→2.15 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3 / Num. unique all: 8870 / Rsym value: 0.362 / % possible all: 71.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→36 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.428 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→36 Å
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