+Open data
-Basic information
Entry | Database: PDB / ID: 2qxw | ||||||
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Title | Perdeuterated alr2 in complex with idd594 | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / NADP / IDD594 / Cataract | ||||||
Function / homology | Function and homology information glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / L-ascorbic acid biosynthetic process / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / epithelial cell maturation / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / electron transfer activity / carbohydrate metabolic process / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.8 Å | ||||||
Authors | Blakeley, M.P. / Ruiz, F. / Cachau, R. / Hazemann, I. / Meilleur, F. / Mitschler, A. / Ginell, S. / Afonine, P. / Ventura, O. / Cousido-Siah, A. ...Blakeley, M.P. / Ruiz, F. / Cachau, R. / Hazemann, I. / Meilleur, F. / Mitschler, A. / Ginell, S. / Afonine, P. / Ventura, O. / Cousido-Siah, A. / Joachimiak, A. / Myles, D. / Podjarny, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase. Authors: Blakeley, M.P. / Ruiz, F. / Cachau, R. / Hazemann, I. / Meilleur, F. / Mitschler, A. / Ginell, S. / Afonine, P. / Ventura, O.N. / Cousido-Siah, A. / Haertlein, M. / Joachimiak, A. / Myles, D. / Podjarny, A. | ||||||
History |
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Remark 999 | sequence The L -> I difference reflects the conflict between different references, as indicated in ...sequence The L -> I difference reflects the conflict between different references, as indicated in UNP entry P15121 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qxw.cif.gz | 183.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qxw.ent.gz | 143.7 KB | Display | PDB format |
PDBx/mmJSON format | 2qxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/2qxw ftp://data.pdbj.org/pub/pdb/validation_reports/qx/2qxw | HTTPS FTP |
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-Related structure data
Related structure data | 2r24C 1usoS S: Starting model for refinement C: citing same article (ref.) |
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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: 35898.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P15121, aldose reductase | ||
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#2: Chemical | ChemComp-NDP / | ||
#3: Chemical | ChemComp-LDT / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.57 % |
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Crystal grow | pH: 5 / Details: 120 mM Ammonium Citrate pH 5.0, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 15 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.653 |
Detector | Type: SBC-2 / Detector: CCD / Date: Nov 7, 2003 Details: 1.02-M FLAT MIRROR MADE OF ZERODUR PROVIDING VERTICAL FOCUSING AND REJECTION OF HARMONIC CONTAMINATION |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR UTILIZING A SI-111 AND SAGITAL HORIZONTAL FOCUSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.653 Å / Relative weight: 1 |
Reflection | Resolution: 0.8→20 Å / Num. obs: 322108 / % possible obs: 99.79 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.65 |
Reflection shell | Resolution: 0.8→0.85 Å / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 2.97 / % possible all: 99.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1USO Resolution: 0.8→10 Å / Num. parameters: 32112 / Num. restraintsaints: 44685 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 166 / Occupancy sum hydrogen: 2413.18 / Occupancy sum non hydrogen: 3026.16 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.8→10 Å
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Refine LS restraints |
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