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Yorodumi- PDB-1sm9: Crystal Structure Of An Engineered K274RN276D Double Mutant of Xy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sm9 | ||||||
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Title | Crystal Structure Of An Engineered K274RN276D Double Mutant of Xylose Reductase From Candida Tenuis Optimized To Utilize NAD | ||||||
Components | xylose reductase | ||||||
Keywords | OXIDOREDUCTASE / xylose metabolism / coenzyme specificity / aldo-keto reductase / beta-alpha-barrel / AKR2B5 | ||||||
Function / homology | Function and homology information D-xylose reductase [NAD(P)H] / D-xylose reductase (NADPH) activity / D-xylose catabolic process / cytosol Similarity search - Function | ||||||
Biological species | Candida tenuis (fungus) | ||||||
Method | X-RAY DIFFRACTION / isomorphous / Resolution: 2.2 Å | ||||||
Authors | Petschacher, B. / Leitgeb, S. / Kavanagh, K.L. / Wilson, D.K. / Nidetzky, B. | ||||||
Citation | Journal: Biochem.J. / Year: 2005 Title: The coenzyme specificity of Candida tenuis xylose reductase (AKR2B5) explored by site-directed mutagenesis and X-ray crystallography. Authors: Petschacher, B. / Leitgeb, S. / Kavanagh, K.L. / Wilson, D.K. / Nidetzky, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sm9.cif.gz | 277.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sm9.ent.gz | 224.1 KB | Display | PDB format |
PDBx/mmJSON format | 1sm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sm9_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1sm9_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1sm9_validation.xml.gz | 56.6 KB | Display | |
Data in CIF | 1sm9_validation.cif.gz | 79.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/1sm9 ftp://data.pdbj.org/pub/pdb/validation_reports/sm/1sm9 | HTTPS FTP |
-Related structure data
Related structure data | 1mi3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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5 |
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6 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36091.199 Da / Num. of mol.: 4 / Mutation: K274R, N276D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida tenuis (fungus) / Plasmid: pBEAct.1i / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: GenBank: 3289019, UniProt: O74237*PLUS, aldose reductase #2: Chemical | ChemComp-NAD / #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: 3.2 Å3/Da / Density % sol: 61.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: ammonium sulfate, sodium acetate, sodium citrate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 11, 2003 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 91362 / Num. obs: 91362 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.51 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous Starting model: wild-type structure of xylose reductase from candida tenuis bound to nad, pdb entry 1MI3 Resolution: 2.2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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