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Yorodumi- PDB-4u8g: Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u8g | ||||||||||||
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Title | Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus agalactiae | ||||||||||||
Components | Putative uncharacterized protein gbs1891 | ||||||||||||
Keywords | OXIDOREDUCTASE / dehydrogenase / SDR family / rosman fold / NADH | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Streptococcus agalactiae NEM316 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||||||||
Authors | Maruyama, Y. / Oiki, S. / Takase, R. / Mikami, B. / Murata, K. / Hashimoto, W. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Metabolic Fate of Unsaturated Glucuronic/Iduronic Acids from Glycosaminoglycans: MOLECULAR IDENTIFICATION AND STRUCTURE DETERMINATION OF STREPTOCOCCAL ISOMERASE AND DEHYDROGENASE. Authors: Maruyama, Y. / Oiki, S. / Takase, R. / Mikami, B. / Murata, K. / Hashimoto, W. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u8g.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u8g.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 4u8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/4u8g ftp://data.pdbj.org/pub/pdb/validation_reports/u8/4u8g | HTTPS FTP |
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-Related structure data
Related structure data | 4u8eC 4u8fC 3cxrS C: citing same article (ref.) 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: 29942.211 Da / Num. of mol.: 1 / Mutation: S150A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae NEM316 (bacteria) Strain: NEM316 / Gene: gbs1891 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8E370 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% polyethylene glycol monomethyl ether 550, 0.1 M sodium chloride, and 0.1 M sodium N,N-bis(2-hydroxyethyl)glycine (pH 9.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 8964 / % possible obs: 99.8 % / Redundancy: 22.5 % / Net I/σ(I): 78.5 |
-Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3cxr Resolution: 2.9→35.64 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.899 / SU B: 14.148 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 75.396 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→35.64 Å
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Refine LS restraints |
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