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Yorodumi- PDB-3ex8: Complex structure of bacillus subtilis RibG reduction mechanism i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ex8 | ||||||
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Title | Complex structure of bacillus subtilis RibG reduction mechanism in riboflavin biosynthesis | ||||||
Components | Riboflavin biosynthesis protein ribD | ||||||
Keywords | HYDROLASE / OXIDOREDUCTASE / alpha/beta/alpha / deaminase domain / reductase domain / Metal-binding / Multifunctional enzyme / NADP / Riboflavin biosynthesis / Zinc | ||||||
Function / homology | Function and homology information 5-amino-6-(5-phosphoribosylamino)uracil reductase / diaminohydroxyphosphoribosylaminopyrimidine deaminase / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / 5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / NADP binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Chen, S.C. / Lin, Y.H. / Yu, H.C. / Liaw, S.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Complex structure of Bacillus subtilis RibG: the reduction mechanism during riboflavin biosynthesis. Authors: Chen, S.C. / Lin, Y.H. / Yu, H.C. / Liaw, S.H. #1: Journal: J.Biol.Chem. / Year: 2006 Title: Crystal structure of a bifunctional deaminase and reductase from Bacillus subtilis involved in riboflavin biosynthesis. Authors: Chen, S.C. / Chang, Y.C. / Lin, C.H. / Liaw, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ex8.cif.gz | 281.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ex8.ent.gz | 226.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ex8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ex8_validation.pdf.gz | 806.8 KB | Display | wwPDB validaton report |
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Full document | 3ex8_full_validation.pdf.gz | 869.1 KB | Display | |
Data in XML | 3ex8_validation.xml.gz | 58.6 KB | Display | |
Data in CIF | 3ex8_validation.cif.gz | 80.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/3ex8 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/3ex8 | HTTPS FTP |
-Related structure data
Related structure data | 2b3zS 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: 40759.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU23280, ribD, ribG / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS References: UniProt: P17618, diaminohydroxyphosphoribosylaminopyrimidine deaminase, 5-amino-6-(5-phosphoribosylamino)uracil reductase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-AIF / [( | #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: 2.71 Å3/Da / Density % sol: 54.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 28 % PEG 400, 200mM CaCl2, 100mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→50 Å / Num. all: 57889 / Num. obs: 56499 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 2.56→2.65 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.7 / Num. unique all: 5437 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B3Z Resolution: 2.56→50 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.56→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.56→2.65 Å
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