+Open data
-Basic information
Entry | Database: PDB / ID: 1y1p | ||||||
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Title | X-ray structure of aldehyde reductase with NADPH | ||||||
Components | Aldehyde reductase II | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / short chain dehydrogenase reductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sporidiobolus salmonicolor (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Kamitori, S. / Kita, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: X-ray Structures of NADPH-dependent Carbonyl Reductase from Sporobolomyces salmonicolor Provide Insights into Stereoselective Reductions of Carbonyl Compounds Authors: Kamitori, S. / Iguchi, A. / Ohtaki, A. / Yamada, M. / Kita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y1p.cif.gz | 162.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y1p.ent.gz | 124.8 KB | Display | PDB format |
PDBx/mmJSON format | 1y1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y1p_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1y1p_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1y1p_validation.xml.gz | 34.5 KB | Display | |
Data in CIF | 1y1p_validation.cif.gz | 51.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/1y1p ftp://data.pdbj.org/pub/pdb/validation_reports/y1/1y1p | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37225.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sporidiobolus salmonicolor (yeast) / Plasmid: pUCAR2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9UUN9, alcohol dehydrogenase (NADP+) |
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-Non-polymers , 6 types, 742 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 32% (w/v) polyethylene glycol 2000 MME, 100mM ammonium sulfate and 200mM sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→74.16 Å / Num. all: 84533 / Num. obs: 84533 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.4 Å2 | |||||||||||||||
Reflection shell | Resolution: 1.6→1.7 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→74.16 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2192638.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.7925 Å2 / ksol: 0.343688 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→74.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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