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- PDB-7cys: Crystal structure of barley agmatine coumaroyltransferase (HvACT)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cys | ||||||
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Title | Crystal structure of barley agmatine coumaroyltransferase (HvACT), an N-acyltransferase in BAHD superfamily | ||||||
![]() | Agmatine coumaroyltransferase-1 | ||||||
![]() | TRANSFERASE / acyltransferase | ||||||
Function / homology | agmatine N4-coumaroyltransferase / agmatine N4-coumaroyltransferase activity / : / Transferase family / Chloramphenicol acetyltransferase-like domain superfamily / Agmatine coumaroyltransferase-1![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamane, M. / Takenoya, M. / Sue, M. / Yajima, S. | ||||||
![]() | ![]() Title: Crystal structure of barley agmatine coumaroyltransferase, an N-acyltransferase from the BAHD superfamily. Authors: Yamane, M. / Takenoya, M. / Yajima, S. / Sue, 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 | ![]() | 107.1 KB | Display | ![]() |
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PDB format | ![]() | 76 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6dd2S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51628.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A9ZPJ6, agmatine N4-coumaroyltransferase |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.08 M sodium cacodylate, pH 6.5, 0.16 M magnesium acetate, 16% (w/v) polyethylene glycol 8,000, and 20% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→50 Å / Num. obs: 44594 / % possible obs: 97.8 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.81→1.85 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2201 / CC1/2: 0.914 / CC star: 0.237 / % possible all: 82.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6dd2 Resolution: 1.81→46.326 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.544 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.109 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.607 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→46.326 Å
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Refine LS restraints |
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LS refinement shell |
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