+Open data
-Basic information
Entry | Database: PDB / ID: 1k02 | ||||||
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Title | Crystal Structure of Old Yellow Enzyme Mutant Gln114Asn | ||||||
Components | NADPH DEHYDROGENASE 1 | ||||||
Keywords | OXIDOREDUCTASE / beta-alpha barrels | ||||||
Function / homology | Function and homology information NADPH dehydrogenase / : / NADPH dehydrogenase activity / FMN binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Brown, B.J. / Hyun, J. / Duvvuri, S.D. / Karplus, P.A. / Massey, V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: The role of glutamine 114 in old yellow enzyme Authors: Brown, B.J. / Hyun, J. / Duvvuri, S.D. / 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 | 1k02.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k02.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 1k02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k02_validation.pdf.gz | 703.5 KB | Display | wwPDB validaton report |
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Full document | 1k02_full_validation.pdf.gz | 713.4 KB | Display | |
Data in XML | 1k02_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 1k02_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/1k02 ftp://data.pdbj.org/pub/pdb/validation_reports/k0/1k02 | HTTPS FTP |
-Related 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: 44926.418 Da / Num. of mol.: 1 / Mutation: Q114N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: Q02899, NADPH dehydrogenase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-FMN / |
#4: 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: 2.42 Å3/Da / Density % sol: 49.25 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: PEG-400, HEPES, Magnesium Chloride, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Details: Fox, K.M., (1993) J. Mol. Biol., 234, 502. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 31, 2000 |
Radiation | Monochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 12522 / Num. obs: 10792 / % possible obs: 85.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.7→2.8 Å / Num. unique all: 1227 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 97.4 % / Num. measured all: 56163 / Rmerge(I) obs: 0.128 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.53 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→500 Å / σ(F): 2 / Stereochemistry target values: EMBL
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Refinement step | Cycle: LAST / Resolution: 2.7→500 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 500 Å / σ(F): 2 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.3 |