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Yorodumi- PDB-1hqt: THE CRYSTAL STRUCTURE OF AN ALDEHYDE REDUCTASE Y50F MUTANT-NADP C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hqt | ||||||
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Title | THE CRYSTAL STRUCTURE OF AN ALDEHYDE REDUCTASE Y50F MUTANT-NADP COMPLEX AND ITS IMPLICATIONS FOR SUBSTRATE BINDING | ||||||
Components | ALDEHYDE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / alpha/beta barrel TIM barrel holo enzyme | ||||||
Function / homology | Function and homology information glucuronate reductase / glucuronolactone reductase / glucuronolactone reductase activity / S-nitrosoglutathione reductase (NADPH) activity / Oxidoreductases; Acting on NADH or NADPH / methylglyoxal reductase (NADPH) (acetol producing) activity / alcohol dehydrogenase (NADP+) / D-glucuronate catabolic process / aldehyde catabolic process / cellular detoxification of aldehyde ...glucuronate reductase / glucuronolactone reductase / glucuronolactone reductase activity / S-nitrosoglutathione reductase (NADPH) activity / Oxidoreductases; Acting on NADH or NADPH / methylglyoxal reductase (NADPH) (acetol producing) activity / alcohol dehydrogenase (NADP+) / D-glucuronate catabolic process / aldehyde catabolic process / cellular detoxification of aldehyde / L-glucuronate reductase activity / glycerol dehydrogenase (NADP+) activity / D/L-glyceraldehyde reductase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / L-ascorbic acid biosynthetic process / aldose reductase (NADPH) activity / lipid metabolic process / apical plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ye, Q. / Hyndman, D. / Green, N.C. / Li, L. / Korithoski, B. / Jia, Z. / Flynn, T.G. | ||||||
Citation | Journal: Chem.Biol.Interact. / Year: 2001 Title: The Crystal Structure of an Aldehyde Reductase Y50F Mutant-NADP Complex and its Implications for Substrate Binding Authors: Ye, Q. / Hyndman, D. / Green, N.C. / Li, L. / Jia, Z. / Flynn, T.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hqt.cif.gz | 84.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hqt.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hqt_validation.pdf.gz | 698.8 KB | Display | wwPDB validaton report |
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Full document | 1hqt_full_validation.pdf.gz | 717.4 KB | Display | |
Data in XML | 1hqt_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 1hqt_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/1hqt ftp://data.pdbj.org/pub/pdb/validation_reports/hq/1hqt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36733.059 Da / Num. of mol.: 1 / Mutation: Y50F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Plasmid: PET16B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P50578, alcohol dehydrogenase (NADP+) |
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#2: Chemical | ChemComp-NAP / |
#3: 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: 2.36 Å3/Da / Density % sol: 47.8 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: evaporation Details: PEG 6000, NaCl, MES, EVAPORATION, temperature 277.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 6.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→6 Å / Num. all: 42437 / Num. obs: 17569 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.072 / Net I/σ(I): 11.04 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.43 / Num. unique all: 17569 / Rsym value: 0.266 / % possible all: 92.6 |
Reflection | *PLUS Num. measured all: 42437 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Ossama EI-Kabbani, personal communication. Resolution: 2.2→6 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→6 Å
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 6 Å / σ(F): 0 / Rfactor obs: 0.212 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.212 |