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Yorodumi- PDB-7dev: Crystal Structures of Anthocyanin 5,3'-aromatic acyltransferase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dev | ||||||
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Title | Crystal Structures of Anthocyanin 5,3'-aromatic acyltransferase from Gentiana triflora | ||||||
Components | Anthocyanin 5-aromatic acyltransferase | ||||||
Keywords | TRANSFERASE / acyltransferase / anthocyanin / plant enzyme / delphinidin / caffeoyl-CoA | ||||||
Function / homology | anthocyanin 5-(6'''-hydroxycinnamoyltransferase) / anthocyanin 5-(6'''-hydroxycinnamoyltransferase) activity / : / : / Chloramphenicol acetyltransferase-like domain superfamily / cytoplasm / Anthocyanin 5-aromatic acyltransferase Function and homology information | ||||||
Biological species | Gentiana triflora (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Murayama, K. / Kato-Murayama, M. / Shirouzu, M. | ||||||
Citation | Journal: Phytochemistry / Year: 2021 Title: Anthocyanin 5,3'-aromatic acyltransferase from Gentiana triflora, a structural insight into biosynthesis of a blue anthocyanin. Authors: Murayama, K. / Kato-Murayama, M. / Sato, T. / Hosaka, T. / Ishiguro, K. / Mizuno, T. / Kitao, K. / Honma, T. / Yokoyama, S. / Tanaka, Y. / Shirouzu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dev.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dev.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 7dev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dev_validation.pdf.gz | 426.1 KB | Display | wwPDB validaton report |
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Full document | 7dev_full_validation.pdf.gz | 434.9 KB | Display | |
Data in XML | 7dev_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 7dev_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/7dev ftp://data.pdbj.org/pub/pdb/validation_reports/de/7dev | HTTPS FTP |
-Related structure data
Related structure data | 7dexC 2e1uS 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: 53421.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gentiana triflora (plant) / Production host: Baculovirus expression vector pCTdual References: UniProt: Q9ZWR8, anthocyanin 5-(6'''-hydroxycinnamoyltransferase) |
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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: 2.61 Å3/Da / Density % sol: 52.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: sodium citrate, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 11, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 10164 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 40.78 Å2 / Rsym value: 0.229 / Net I/σ(I): 10.47 |
Reflection shell | Resolution: 3.1→3.21 Å / Num. unique obs: 991 / Rsym value: 0.777 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E1U Resolution: 3.1→49.54 Å / SU ML: 0.3738 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8398 / Stereochemistry target values: GeoStd + Monomer Library
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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 mean: 40.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→49.54 Å
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Refine LS restraints |
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LS refinement shell |
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