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Yorodumi- PDB-1r9d: Glycerol bound form of the B12-independent glycerol dehydratase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r9d | ||||||
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Title | Glycerol bound form of the B12-independent glycerol dehydratase from Clostridium butyricum | ||||||
Components | glycerol dehydratase | ||||||
Keywords | LYASE / glycerol dehydratase / radical SAM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium butyricum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Lanzilotta, W.N. / O'Brien, J.R. / Raynaud, C. / Soucaille, P. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Insight into the mechanism of the B12-independent glycerol dehydratase from Clostridium butyricum: preliminary biochemical and structural characterization. Authors: O'Brien, J.R. / Raynaud, C. / Croux, C. / Girbal, L. / Soucaille, P. / Lanzilotta, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r9d.cif.gz | 327.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r9d.ent.gz | 264.2 KB | Display | PDB format |
PDBx/mmJSON format | 1r9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/1r9d ftp://data.pdbj.org/pub/pdb/validation_reports/r9/1r9d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The file contains the asymmetric unit, which is also proposed to be the physiological dimer |
-Components
#1: Protein | Mass: 88154.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium butyricum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GEZ8 #2: Chemical | #3: 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: 3.11 Å3/Da / Density % sol: 60.48 % |
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Crystal grow | Temperature: 270 K / Method: capillary batch / pH: 6.5 Details: PEG 3350, tri-ammonium citrate, pH 6.5, capillary batch, temperature 270K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2003 |
Radiation | Monochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 199038 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.08 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 1.8→1.91 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.28 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.91 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 4580453.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.813 Å2 / ksol: 0.34568 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→49.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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