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Yorodumi- PDB-1z9a: Crystal Structure Of The Asn-309 To Asp Mutant Of Candida Tenuis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z9a | ||||||
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Title | Crystal Structure Of The Asn-309 To Asp 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 / xylose reductase / candida tenuis / substrate selectivity / ketone reduction / structure-activity correlation | ||||||
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: 2.4 Å | ||||||
Authors | Kratzer, R. / Leitgeb, S. / Wilson, D.K. / Nidetzky, B. | ||||||
Citation | Journal: Biochem.J. / Year: 2006 Title: Probing the substrate binding site of Candida tenuis xylose reductase (AKR2B5) with site-directed mutagenesis Authors: Kratzer, R. / Leitgeb, S. / 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 | 1z9a.cif.gz | 277.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z9a.ent.gz | 224.2 KB | Display | PDB format |
PDBx/mmJSON format | 1z9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z9a_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1z9a_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1z9a_validation.xml.gz | 56.6 KB | Display | |
Data in CIF | 1z9a_validation.cif.gz | 79.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/1z9a ftp://data.pdbj.org/pub/pdb/validation_reports/z9/1z9a | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35931.992 Da / Num. of mol.: 4 / Mutation: N310D 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): BL21(DE3) References: UniProt: O74237, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor #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: 3.23 Å3/Da / Density % sol: 61.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: ammonium sulfate, sodium acetate, sodium citrate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: Jan 28, 2004 |
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: 2.4→30 Å / Num. all: 64303 / Num. obs: 64303 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.17 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3.2 / % possible all: 82.9 |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous Starting model: candida tenuis xylose reductase bound to nad Resolution: 2.4→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Xplor file |
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