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Yorodumi- PDB-4hbg: Crystal structure of Saccharomyces cerevisiae 3 oxoacyl-[acyl car... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hbg | ||||||
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Title | Crystal structure of Saccharomyces cerevisiae 3 oxoacyl-[acyl carrier protein]-reductase complexed with NADPH (form2) | ||||||
Components | 3-oxoacyl-[acyl-carrier-protein] reductase | ||||||
Keywords | OXIDOREDUCTASE / short-chain alcohol dehydrogenase (SDR) family / Fatty acid synthetase / NADPH / mitochondrial FAS II pathway | ||||||
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 / aerobic respiration / fatty acid metabolic process / fatty acid biosynthetic process / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Zhang, Y.J. / Gao, Y.X. / Teng, M.K. | ||||||
Citation | Journal: To be Published Title: Crystal structure of yeast mitochondria 3-Oxoacyl-ACP Reductase OAR1 Authors: Zhang, Y.J. / Gao, Y.X. / Teng, M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hbg.cif.gz | 111.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hbg.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 4hbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/4hbg ftp://data.pdbj.org/pub/pdb/validation_reports/hb/4hbg | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32291.121 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 |
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#2: Chemical | ChemComp-NDP / |
#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: 2.39 Å3/Da / Density % sol: 48.62 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% V/V JEFFAMINE ED2001, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2011 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→50 Å / Num. all: 15308 / Num. obs: 14440 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.066 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→41.93 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.734 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 52.767 Å2
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Refinement step | Cycle: LAST / Resolution: 2.27→41.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.333 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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