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Yorodumi- PDB-1ye4: Crystal structure of the Lys-274 to Arg mutant of Candida tenuis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ye4 | ||||||
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Title | Crystal structure of the Lys-274 to Arg mutant of Candida tenuis xylose reductase (AKR2B5) bound to NAD+ | ||||||
Components | NAD(P)H-dependent D-xylose reductase | ||||||
Keywords | OXIDOREDUCTASE / beta-alpha-barrel AKR aldo-keto reductase coenzyme specificity NAD | ||||||
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 / SYNCHROTRON / isomourphous / Resolution: 2.4 Å | ||||||
Authors | Leitgeb, S. / Petschacher, B. / Wilson, D.K. / Nidetzky, B. | ||||||
Citation | Journal: FEBS Lett. / Year: 2005 Title: Fine tuning of coenzyme specificity in family 2 aldo-keto reductases revealed by crystal structures of the Lys-274-->Arg mutant of Candida tenuis xylose reductase (AKR2B5) bound to NAD(+) and NADP(+). Authors: Leitgeb, S. / Petschacher, B. / 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 | 1ye4.cif.gz | 275.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ye4.ent.gz | 223 KB | Display | PDB format |
PDBx/mmJSON format | 1ye4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ye4_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1ye4_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1ye4_validation.xml.gz | 55.8 KB | Display | |
Data in CIF | 1ye4_validation.cif.gz | 77.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/1ye4 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/1ye4 | HTTPS FTP |
-Related structure data
Related structure data | 1ye6C 1mi3S 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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Unit cell |
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-Components
#1: Protein | Mass: 36090.215 Da / Num. of mol.: 4 / Mutation: K274R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida tenuis (fungus) / Gene: XYL1, XYLR / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21(DE3) References: UniProt: O74237, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NAD / #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: 3.26 Å3/Da / Density % sol: 62.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: Ammonium sulfate, sodium citrate, , pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.953695 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 9, 2004 |
Radiation | Monochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953695 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 69609 / Num. obs: 69609 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.61 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 3.21 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: isomourphous Starting model: PDB ENTRY 1MI3 Resolution: 2.4→30 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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