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Yorodumi- PDB-1mi3: 1.8 Angstrom structure of xylose reductase from Candida tenuis in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mi3 | ||||||
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Title | 1.8 Angstrom structure of xylose reductase from Candida tenuis in complex with NAD | ||||||
Components | xylose reductase | ||||||
Keywords | OXIDOREDUCTASE / aldo-keto reductase / beta-alpha barrel / dimer | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kavanagh, K.L. / Klimacek, M. / Nidetzky, B. / Wilson, D.K. | ||||||
Citation | Journal: Biochem.J. / Year: 2003 Title: Structure of xylose reductase bound to NAD+ and the basis for single and dual co-substrate specificity in family 2 aldo-keto reductases Authors: Kavanagh, K.L. / Klimacek, M. / Nidetzky, B. / Wilson, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mi3.cif.gz | 277.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mi3.ent.gz | 224.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mi3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mi3_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1mi3_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1mi3_validation.xml.gz | 55.3 KB | Display | |
Data in CIF | 1mi3_validation.cif.gz | 79.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/1mi3 ftp://data.pdbj.org/pub/pdb/validation_reports/mi/1mi3 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-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: 36062.199 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida tenuis (fungus) / Gene: xylR / Plasmid: pBEAct.1i / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O74237, 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: 2.95 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 32% PEG-ME 5K, 350 mM ammonium sulfate, 100 mM sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 2, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 164527 / Num. obs: 162718 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3 / % possible all: 98.2 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 162716 / Num. measured all: 728917 |
Reflection shell | *PLUS % possible obs: 98.2 % / Mean I/σ(I) obs: 3.02 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: unpublished model of XR mutant Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. reflection obs: 154541 / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.183 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.7 |