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Yorodumi- PDB-6k3c: Crystal structure of class I PHA synthase (PhaC) mutant from Chro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k3c | ||||||
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Title | Crystal structure of class I PHA synthase (PhaC) mutant from Chromobacterium sp. USM2 bound to Coenzyme A. | ||||||
Components | Intracellular polyhydroxyalkanoate synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Bioplastic synthase / catalytic domain / CoA binding. / open conformation / open-closed dimer | ||||||
Function / homology | Function and homology information poly-hydroxybutyrate biosynthetic process / acyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Chromobacterium sp. USM2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.074 Å | ||||||
Authors | Chek, M.F. / Kim, S.Y. / Mori, T. / Hakoshima, T. | ||||||
Citation | Journal: Iscience / Year: 2020 Title: Asymmetric Open-Closed Dimer Mechanism of Polyhydroxyalkanoate Synthase PhaC. Authors: Chek, M.F. / Kim, S.Y. / Mori, T. / Tan, H.T. / Sudesh, K. / Hakoshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k3c.cif.gz | 159.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k3c.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 6k3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k3c_validation.pdf.gz | 703.1 KB | Display | wwPDB validaton report |
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Full document | 6k3c_full_validation.pdf.gz | 711.6 KB | Display | |
Data in XML | 6k3c_validation.xml.gz | 28 KB | Display | |
Data in CIF | 6k3c_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/6k3c ftp://data.pdbj.org/pub/pdb/validation_reports/k3/6k3c | HTTPS FTP |
-Related structure data
Related structure data | 5xavS 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: 43828.410 Da / Num. of mol.: 2 / Mutation: D447N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium sp. USM2 (bacteria) / Gene: phaC / Production host: Escherichia coli (E. coli) / References: UniProt: E1APK1 #2: Chemical | ChemComp-COA / | #3: Water | ChemComp-HOH / | |
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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: 2.37 Å3/Da / Density % sol: 48.07 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Sodium acetate, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97914 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 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: 3.074→50 Å / Num. obs: 15234 / % possible obs: 96.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 3.074→3.15 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.513 / Num. unique obs: 1912 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XAV Resolution: 3.074→49.953 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.074→49.953 Å
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Refine LS restraints |
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LS refinement shell |
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