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Yorodumi- PDB-8h6s: Structure of acyltransferase VinK in complex with the loading acy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h6s | |||||||||
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Title | Structure of acyltransferase VinK in complex with the loading acyl carrier protein of vicenistatin PKS | |||||||||
Components |
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Keywords | TRANSFERASE / acyl carrier protein / polyketide synthase / acyltransferase | |||||||||
Function / homology | Function and homology information polyketide biosynthetic process / : / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / oxidoreductase activity / zinc ion binding ...polyketide biosynthetic process / : / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / oxidoreductase activity / zinc ion binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Streptomyces halstedii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Kawada, K. / Miyanaga, A. / Chisuga, T. / Kudo, F. / Eguchi, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Biochemistry / Year: 2023 Title: Structural Basis of Transient Interactions of Acyltransferase VinK with the Loading Acyl Carrier Protein of the Vicenistatin Modular Polyketide Synthase. Authors: Miyanaga, A. / Kawada, K. / Chisuga, T. / Kudo, F. / Eguchi, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h6s.cif.gz | 168.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h6s.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 8h6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h6s_validation.pdf.gz | 828.6 KB | Display | wwPDB validaton report |
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Full document | 8h6s_full_validation.pdf.gz | 833.8 KB | Display | |
Data in XML | 8h6s_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 8h6s_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/8h6s ftp://data.pdbj.org/pub/pdb/validation_reports/h6/8h6s | HTTPS FTP |
-Related structure data
Related structure data | 5czdS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 38170.211 Da / Num. of mol.: 2 / Mutation: S106C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinK / Plasmid: pCold I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76KY5 #2: Protein | Mass: 14712.665 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinP1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76KY0 #3: Chemical | #4: Chemical | #5: 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 % sol: 35.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 4000, magnesium chloride, Tris-HCl, and D-glucose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2019 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 16764 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.173 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2385 / CC1/2: 0.735 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CZD Resolution: 3→46.01 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / SU B: 27.672 / SU ML: 0.462 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 145.81 Å2 / Biso mean: 64.029 Å2 / Biso min: 23.03 Å2
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Refinement step | Cycle: final / Resolution: 3→46.01 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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