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Yorodumi- PDB-4rji: Acetolactate synthase from Bacillus subtilis bound to ThDP - crys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rji | ||||||
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Title | Acetolactate synthase from Bacillus subtilis bound to ThDP - crystal form I | ||||||
Components | Acetolactate synthase | ||||||
Keywords | LYASE / ThDP | ||||||
Function / homology | Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / THIAMINE DIPHOSPHATE / : Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Sommer, B. / von Moeller, H. / Haack, M. / Qoura, F. / Langner, C. / Bourenkov, G. / Garbe, D. / Brueck, T. / Loll, B. | ||||||
Citation | Journal: Chembiochem / Year: 2015 Title: Detailed Structure-Function Correlations of Bacillus subtilis Acetolactate Synthase. Authors: Sommer, B. / von Moeller, H. / Haack, M. / Qoura, F. / Langner, C. / Bourenkov, G. / Garbe, D. / Loll, B. / Bruck, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rji.cif.gz | 425.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rji.ent.gz | 345.8 KB | Display | PDB format |
PDBx/mmJSON format | 4rji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rji_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4rji_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4rji_validation.xml.gz | 74.7 KB | Display | |
Data in CIF | 4rji_validation.cif.gz | 99 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/4rji ftp://data.pdbj.org/pub/pdb/validation_reports/rj/4rji | HTTPS FTP |
-Related structure data
Related structure data | 4rjjC 4rjkC 1ozfS 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: 63970.750 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: PY79 / Gene: U712_18080 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: V5MX36, EC: 4.1.3.18 #2: Chemical | ChemComp-TPP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-PG4 / | #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: 2.31 Å3/Da / Density % sol: 46.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30 % (v/v) polyethylene glycol 300, 200 mM Ca acetate, 100 mM Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 19, 2012 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 40326 / Num. obs: 40142 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 53.6 Å2 |
Reflection shell | Resolution: 3.2→3.39 Å / Redundancy: 7.1 % / % possible all: 98.9 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OZF Resolution: 3.2→29.664 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 24.27 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→29.664 Å
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Refine LS restraints |
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LS refinement shell |
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