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Yorodumi- PDB-6iyr: Crystal Structure of the acyltransferase domain from module 8 of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iyr | ||||||
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Title | Crystal Structure of the acyltransferase domain from module 8 of the salinomycin polyketide synthase | ||||||
Components | Type I modular polyketide synthase | ||||||
Keywords | TRANSFERASE / acyltransferase / malonyl-coenzyme A / polyketide | ||||||
Function / homology | Function and homology information macrolide biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Streptomyces albus subsp. albus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Zhang, F. / Zheng, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochemistry / Year: 2019 Title: Structural Insights into the Substrate Specificity of Acyltransferases from Salinomycin Polyketide Synthase. Authors: Zhang, F. / Shi, T. / Ji, H. / Ali, I. / Huang, S. / Deng, Z. / Min, Q. / Bai, L. / Zhao, Y. / Zheng, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iyr.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iyr.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 6iyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/6iyr ftp://data.pdbj.org/pub/pdb/validation_reports/iy/6iyr | HTTPS FTP |
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-Related structure data
Related structure data | 6iyoC 6iytC 2hg4S 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: 48997.930 Da / Num. of mol.: 1 / Fragment: UNP residues 480-929 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces albus subsp. albus (bacteria) Gene: salAV / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: H1ZZT7 |
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#2: Chemical | ChemComp-PO4 / |
#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: 3.04 Å3/Da / Density % sol: 59.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.2 / Details: 0.056M NaH2PO4, 1.544M K2HPO4 pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 36404 / % possible obs: 99.93 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 56.4 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 2628 / % possible all: 99.68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HG4 Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.054 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.149 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.968 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→50 Å
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Refine LS restraints |
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