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Yorodumi- PDB-4j1s: Crystal structure of a ketoreductase domain from the bacillaene a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j1s | ||||||
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Title | Crystal structure of a ketoreductase domain from the bacillaene assembly line | ||||||
Components | Polyketide synthase PksJ | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / ketoreductase | ||||||
Function / homology | Function and homology information DIM/DIP cell wall layer assembly / organonitrogen compound biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / ligase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Zheng, J. / Keatinge-Clay, A.T. | ||||||
Citation | Journal: Proteins / Year: 2014 Title: Structural and functional studies of a trans-acyltransferase polyketide assembly line enzyme that catalyzes stereoselective alpha- and beta-ketoreduction. Authors: Piasecki, S.K. / Zheng, J. / Axelrod, A.J. / E Detelich, M. / Keatinge-Clay, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j1s.cif.gz | 181.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j1s.ent.gz | 145.4 KB | Display | PDB format |
PDBx/mmJSON format | 4j1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/4j1s ftp://data.pdbj.org/pub/pdb/validation_reports/j1/4j1s | HTTPS FTP |
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-Related structure data
Related structure data | 4j1qSC S: Starting model for refinement C: citing same article (ref.) |
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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: 52515.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: BSU17180, pksJ, pksJ (amino acids 2669-3111), pksK / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P40806, 3-oxoacyl-[acyl-carrier-protein] reductase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris, 25% PEG 1000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979468 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2012 |
Radiation | Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979468 Å / Relative weight: 1 |
Reflection | Resolution: 3→51.57 Å / Num. all: 8868 / Num. obs: 8859 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 4.6 / Num. unique all: 427 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J1Q Resolution: 3.01→51.57 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.877 / SU B: 53.963 / SU ML: 0.429 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.51 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.445 Å2
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Refinement step | Cycle: LAST / Resolution: 3.01→51.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.006→3.084 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 13.0677 Å / Origin y: 9.4783 Å / Origin z: 107.396 Å
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