+Open data
-Basic information
Entry | Database: PDB / ID: 1bwk | ||||||
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Title | OLD YELLOW ENZYME (OYE1) MUTANT H191N | ||||||
Components | PROTEIN (NADPH DEHYDROGENASE 1) | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / NADPH OXIDOREDUCTASE / TIM BARREL | ||||||
Function / homology | Function and homology information NADPH dehydrogenase / : / NADPH dehydrogenase activity / FMN binding / cytosol Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å | ||||||
Authors | Brown, B.J. / Deng, Z. / Karplus, P.A. / Massey, V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: On the active site of Old Yellow Enzyme. Role of histidine 191 and asparagine 194. Authors: Brown, B.J. / Deng, Z. / Karplus, P.A. / Massey, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bwk.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bwk.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 1bwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bwk_validation.pdf.gz | 455.5 KB | Display | wwPDB validaton report |
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Full document | 1bwk_full_validation.pdf.gz | 461.5 KB | Display | |
Data in XML | 1bwk_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 1bwk_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/1bwk ftp://data.pdbj.org/pub/pdb/validation_reports/bw/1bwk | HTTPS FTP |
-Related structure data
Related structure data | 1bwlC 1oyaS 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: 44874.297 Da / Num. of mol.: 1 / Mutation: H191N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Gene: OYE1 / Plasmid: PET3B / Gene (production host): OYE1-H191N / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE / 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.97 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.3 / Details: pH 8.3 | ||||||||||||||||||||||||||||||||||||||||||||||||
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
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR |
Radiation | 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→25 Å / Num. obs: 20012 / % possible obs: 97.1 % / Redundancy: 3.8 % / Rsym value: 0.084 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.3→2.4 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.383 / % possible all: 96.1 |
Reflection | *PLUS Num. measured all: 76546 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 96.1 % / Rmerge(I) obs: 0.383 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1OYA Resolution: 2.3→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.0001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 21.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 8 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Rfactor Rfree: 0.367 / Rfactor Rwork: 0.265 |