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Yorodumi- PDB-8aw0: Crystal structure of PksD, the trans-acting acyl hydrolase domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aw0 | ||||||
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Title | Crystal structure of PksD, the trans-acting acyl hydrolase domain from the bacillaene trans-AT PKS (native) | ||||||
Components | Polyketide biosynthesis acyltransferase homolog PksD | ||||||
Keywords | HYDROLASE / alpha/beta-hydrolase / acyltransferase / polyketide synthase / biosynthesis | ||||||
Function / homology | Function and homology information acyltransferase activity / antibiotic biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Fage, C.D. / Challis, G.L. / Lewandowski, J. / Jenner, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Structural basis for acyl hydrolysis in trans-AT polyketide synthases Authors: Fage, C.D. / Passmore, M. / Tatman, B. / Smith, H.G. / Jian, X. / Mudiyanselage, U.C.M. / Berger, M. / Cisneros, A.G. / Challis, G.L. / Lewandowski, J.R. / Jenner, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aw0.cif.gz | 510.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aw0.ent.gz | 421.8 KB | Display | PDB format |
PDBx/mmJSON format | 8aw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aw0_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 8aw0_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8aw0_validation.xml.gz | 88 KB | Display | |
Data in CIF | 8aw0_validation.cif.gz | 122.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/8aw0 ftp://data.pdbj.org/pub/pdb/validation_reports/aw/8aw0 | HTTPS FTP |
-Related structure data
Related structure data | 8avzC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 37136.457 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: PksD, with an N-terminal Gly-Ser-His thrombin cleavage scar Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Strain: 168 / Gene: pksD, BSU17110 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O34877, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.76 Å3/Da / Density % sol: 67.28 % / Description: Rectangular prism |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 10% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 2, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97628 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→90.46 Å / Num. obs: 220807 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 15.2 / Num. measured all: 1524232 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SeMet-derived PksD Resolution: 2.2→51.08 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.13 / 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: 179.93 Å2 / Biso mean: 75.4819 Å2 / Biso min: 40.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→51.08 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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