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Yorodumi- PDB-1oya: OLD YELLOW ENZYME AT 2 ANGSTROMS RESOLUTION: OVERALL STRUCTURE, L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oya | ||||||
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Title | OLD YELLOW ENZYME AT 2 ANGSTROMS RESOLUTION: OVERALL STRUCTURE, LIGAND BINDING AND COMPARISON WITH RELATED FLAVOPROTEINS | ||||||
Components | OLD YELLOW ENZYMENADPH dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE (FLAVOPROTEIN) | ||||||
Function / homology | Function and homology information NADPH dehydrogenase / pentaerythritol trinitrate reductase activity / NADPH dehydrogenase activity / FMN binding Similarity search - Function | ||||||
Biological species | Saccharomyces pastorianus (lager yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Fox, K.M. / Karplus, P.A. | ||||||
Citation | Journal: Structure / Year: 1994 Title: Old yellow enzyme at 2 A resolution: overall structure, ligand binding, and comparison with related flavoproteins. Authors: Fox, K.M. / Karplus, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oya.cif.gz | 93.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oya.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 1oya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/1oya ftp://data.pdbj.org/pub/pdb/validation_reports/oy/1oya | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 44 |
-Components
#1: Protein | Mass: 45071.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces pastorianus (lager yeast) Gene: OYE1 / Plasmid: PET / References: UniProt: Q02899, NADPH dehydrogenase |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.47 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Fox, K.M., (1993) J. Mol. Biol., 234, 502. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 28528 / % possible obs: 91.1 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Redundancy: 2.3 % / Rmerge(I) obs: 0.04 |
-Processing
Software |
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Refinement | Resolution: 2→10 Å
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Displacement parameters | Biso mean: 18 Å2 | ||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refinement | *PLUS | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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