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Yorodumi- PDB-3du4: Crystal structure of 7-keto-8-aminopelargonic acid bound 7,8-diam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3du4 | ||||||
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Title | Crystal structure of 7-keto-8-aminopelargonic acid bound 7,8-diaminopelargonic acid synthase in bacillus subtilis | ||||||
Components | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | ||||||
Keywords | TRANSFERASE / aminotransferase / biotin biosynthesis / pyridoxal phosphate / s-adenosyl-l-methionine / 7-keto / 8-amino pelargonic acid | ||||||
Function / homology | Function and homology information lysine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / dethiobiotin synthase activity / biotin biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dey, S. / Sacchettini, J.C. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase . Authors: Dey, S. / Lane, J.M. / Lee, R.E. / Rubin, E.J. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3du4.cif.gz | 189.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3du4.ent.gz | 150.8 KB | Display | PDB format |
PDBx/mmJSON format | 3du4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3du4_validation.pdf.gz | 473.3 KB | Display | wwPDB validaton report |
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Full document | 3du4_full_validation.pdf.gz | 498.3 KB | Display | |
Data in XML | 3du4_validation.xml.gz | 38 KB | Display | |
Data in CIF | 3du4_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/3du4 ftp://data.pdbj.org/pub/pdb/validation_reports/du/3du4 | HTTPS FTP |
-Related structure data
Related structure data | 3bv0C 3dodSC 3drdC 3fgnC 3fmfC 3fmiC 3fpaC 3lv2C S: Starting model for refinement C: citing same article (ref.) |
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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: 50190.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: bioA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P53555, adenosylmethionine-8-amino-7-oxononanoate transaminase #2: Chemical | #3: Chemical | #4: 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: 2.19 Å3/Da / Density % sol: 43.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG3350, 0.2M SODIUM THIOCYANATE, 5% XYLITOL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→72 Å / Num. obs: 43651 / % possible obs: 99.4 % / Redundancy: 4.22 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.8 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DOD Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.311 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 28.685 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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