+Open data
-Basic information
Entry | Database: PDB / ID: 1wnt | ||||||
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Title | Structure of the tetrameric form of Human L-Xylulose Reductase | ||||||
Components | L-xylulose reductase | ||||||
Keywords | OXIDOREDUCTASE / 7 stranded parallel beta sheets / 6 alpha helices / Rossmann fold / dinucleotide co-enzyme binding motif | ||||||
Function / homology | Function and homology information Essential pentosuria / L-xylulose reductase / L-xylulose reductase (NADPH) activity / xylulose metabolic process / glucuronate catabolic process to xylulose 5-phosphate / Formation of xylulose-5-phosphate / carbonyl reductase (NADPH) activity / NADP metabolic process / D-xylose metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor ...Essential pentosuria / L-xylulose reductase / L-xylulose reductase (NADPH) activity / xylulose metabolic process / glucuronate catabolic process to xylulose 5-phosphate / Formation of xylulose-5-phosphate / carbonyl reductase (NADPH) activity / NADP metabolic process / D-xylose metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / microvillus / brush border / cytoplasmic microtubule / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | El-Kabbani, O. / Carbone, V. / Darmanin, C. / Ishikura, S. / Hara, A. | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Structure of the tetrameric form of human L-Xylulose reductase: Probing the inhibitor-binding site with molecular modeling and site-directed mutagenesis Authors: El-Kabbani, O. / Carbone, V. / Darmanin, C. / Ishikura, S. / Hara, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wnt.cif.gz | 195.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wnt.ent.gz | 157.3 KB | Display | PDB format |
PDBx/mmJSON format | 1wnt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/1wnt ftp://data.pdbj.org/pub/pdb/validation_reports/wn/1wnt | HTTPS FTP |
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-Related structure data
Related structure data | 1pr9S 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: 25941.033 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: kidney / Plasmid: pRset / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7Z4W1, L-xylulose reductase #2: Chemical | ChemComp-NAP / #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: 2.1 Å3/Da / Density % sol: 41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, Sodium Citrate, Isopropanol, Urea, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-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: Aug 10, 2003 / Details: mirrors |
Radiation | Monochromator: Capillary optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 64193 / Num. obs: 32262 / % possible obs: 92 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 1.99 % / Rsym value: 0.09 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.98 / Rsym value: 0.346 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: XR dimer (1PR9) Resolution: 2.3→12 Å / Isotropic thermal model: Isotropic / σ(F): 4 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→12 Å
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Refine LS restraints |
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