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- PDB-7dex: Crystal Structures of Anthocyanin 5,3'-aromatic acyltransferase H... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dex | ||||||
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Title | Crystal Structures of Anthocyanin 5,3'-aromatic acyltransferase H174A mutant with caffeoyl-CoA | ||||||
![]() | Anthocyanin 5-aromatic acyltransferase | ||||||
![]() | 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 / Chem-H5L / Anthocyanin 5-aromatic acyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Murayama, K. / Kato-Murayama, M. / Shirouzu, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.1 KB | Display | ![]() |
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PDB format | ![]() | 81 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 624.8 KB | Display | ![]() |
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Full document | ![]() | 637.5 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7devC ![]() 2e1uS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 52339.984 Da / Num. of mol.: 1 / Mutation: H174A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9ZWR8, anthocyanin 5-(6'''-hydroxycinnamoyltransferase) |
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#2: Chemical | ChemComp-H5L / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Hepes, sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.65 Å / Num. obs: 19939 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 51.12 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Rmerge(I) obs: 1.107 / Num. unique obs: 2826 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2E1U Resolution: 2.5→29.65 Å / SU ML: 0.3628 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.7564 / 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: 57.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.65 Å
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Refine LS restraints |
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LS refinement shell |
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