+Open data
-Basic information
Entry | Database: PDB / ID: 3woh | |||||||||
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Title | Structure of Ketoreductase SiaM from Streptomyces sp. A7248 | |||||||||
Components | SiaM | |||||||||
Keywords | OXIDOREDUCTASE / enzyme / tetramer / ketoreductase / ACP / Reduction | |||||||||
Function / homology | Function and homology information : / : / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid biosynthetic process / NAD binding Similarity search - Function | |||||||||
Biological species | Streptomyces (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Wang, H. / Zhang, H. | |||||||||
Citation | Journal: Plos One / Year: 2014 Title: Structural insight into the tetramerization of an iterative ketoreductase siam through aromatic residues in the interfaces Authors: Wang, H. / Zhang, H. / Zou, Y. / Mi, Y. / Lin, S. / Xie, Z. / Yan, Y. / Zhang, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3woh.cif.gz | 99.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3woh.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 3woh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/3woh ftp://data.pdbj.org/pub/pdb/validation_reports/wo/3woh | HTTPS FTP |
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-Related structure data
Related structure data | 2uvdS S: Starting model for refinement |
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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: 26077.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces (bacteria) / Strain: A7248 / Production host: Escherichia coli (E. coli) / References: UniProt: K9M8L2 |
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#2: 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: 1.89 Å3/Da / Density % sol: 34.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1.5M Ammonium sulfate, 0.1M Tris, 12%(v/v) Glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→51.274 Å / Num. all: 7354 / Num. obs: 7354 / % possible obs: 75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9 % / Biso Wilson estimate: 46.72 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2UVD Resolution: 2.5→51.274 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7203 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 30.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.09 Å2 / Biso mean: 67.4637 Å2 / Biso min: 26.11 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→51.274 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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Refinement TLS params. | Method: refined / Origin x: 18.6926 Å / Origin y: -16.2395 Å / Origin z: -15.4302 Å
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Refinement TLS group | Selection details: ALL |