[English] 日本語
Yorodumi- PDB-1k03: Crystal Structure of Old Yellow Enzyme Mutant Gln114Asn Complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k03 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Old Yellow Enzyme Mutant Gln114Asn Complexed with Para-hydroxy Benzaldehyde | ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1k03.cif.gz | 102.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1k03.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 1k03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k03_validation.pdf.gz | 725.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1k03_full_validation.pdf.gz | 730.1 KB | Display | |
Data in XML | 1k03_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 1k03_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/1k03 ftp://data.pdbj.org/pub/pdb/validation_reports/k0/1k03 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-FMN / |
#4: Chemical | ChemComp-HBA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.72 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: PEG-400, HEPES, Magnesium chloride, para-hydroxy benzaldehyde, 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
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 2, 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: 12717 / Num. obs: 10862 / % possible obs: 84.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.7→2.8 Å / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 99.4 % / Num. measured all: 53389 / Rmerge(I) obs: 0.135 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.563 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→500 Å / σ(F): 2 / Stereochemistry target values: EMBL
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→500 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 500 Å / σ(F): 2 / Rfactor obs: 0.132 / Rfactor Rwork: 0.13 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.3 |