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- PDB-7ovu: Crystal structure of Arabidopsis thaliana NAT9 in complex with AcCoA -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ovu | |||||||||
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Title | Crystal structure of Arabidopsis thaliana NAT9 in complex with AcCoA | |||||||||
![]() | Acyl-CoA N-acyltransferases (NAT) superfamily protein | |||||||||
![]() | PLANT PROTEIN / GNAT N-acetyltransferase AcCoA PLANT PROTEIN NAT9 | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Layer, D. / Weyer, F.A. / Kopp, J. / Sinning, I. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the Arabidopsis thaliana N-acetyltransferase 9 Authors: Layer, D. / Weyer, F.A. / Kopp, J. / Sinning, I. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.9 KB | Display | ![]() |
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PDB format | ![]() | 105.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 739.4 KB | Display | ![]() |
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Full document | ![]() | 740.9 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3eo4S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 24560.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ACO / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: AtNAT9 was concentrated to 15 mg/ml and incubated with a threefold molar excess of AcCoA for 18 h on ice. Crystallization drops contained 200 nl protein solution and 200 nl precipitant ...Details: AtNAT9 was concentrated to 15 mg/ml and incubated with a threefold molar excess of AcCoA for 18 h on ice. Crystallization drops contained 200 nl protein solution and 200 nl precipitant solution (0.1 M HEPES (pH 7) and 20 % PEG6000) and crystals appeared after seven days. The crystals were cryo-protected with 20 % glycerol and flash-frozen in liquid nitrogen. |
-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: Dec 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→39.19 Å / Num. obs: 33777 / % possible obs: 99.7 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.45→1.5 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3306 / CC1/2: 0.509 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3eo4 Resolution: 1.45→39.19 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.11 / Stereochemistry target values: ML
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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 max: 93.41 Å2 / Biso mean: 30.7526 Å2 / Biso min: 15.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→39.19 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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