[English] 日本語
Yorodumi- PDB-4fda: Crystal structure of Saccharomyces cerevisiae 3-oxoacyl-[acyl-car... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fda | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Saccharomyces cerevisiae 3-oxoacyl-[acyl-carrier-protein] reductase complexed with NADP | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] reductase | ||||||
Keywords | OXIDOREDUCTASE / short-chain alcohol dehydrogenase (SDR) family | ||||||
Function / homology | Function and homology information Fatty acyl-CoA biosynthesis / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / quinone binding / fatty acid metabolic process / aerobic respiration / fatty acid biosynthetic process / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Yujie, Z. / Yongxiang, G. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Saccharomyces cerevisiae 3-oxoacyl-[acyl-carrier-protein] reductase complexed with NADPH Authors: Yujie, Z. / Yongxiang, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4fda.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4fda.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 4fda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fda_validation.pdf.gz | 787.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4fda_full_validation.pdf.gz | 793.6 KB | Display | |
Data in XML | 4fda_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 4fda_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/4fda ftp://data.pdbj.org/pub/pdb/validation_reports/fd/4fda | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 30704.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: OAR1, YKL055C / Production host: Escherichia coli (E. coli) References: UniProt: P35731, 3-oxoacyl-[acyl-carrier-protein] reductase |
---|---|
#2: Chemical | ChemComp-NAP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.15 % |
---|---|
Crystal grow | Temperature: 285 K / Method: vapor diffusion / pH: 7 Details: 10% PEG 4000, 10% 2-propanol, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 23828 / Observed criterion σ(F): 5 / Observed criterion σ(I): 2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.711 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.053 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.096→2.15 Å / Total num. of bins used: 20
|