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Open data
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Basic information
Entry | Database: PDB / ID: 7pk1 | ||||||
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Title | Bovine Glycine N-Acyltransferase | ||||||
![]() | Glycine N-acyltransferase | ||||||
![]() | TRANSFERASE / GLYAT / glycine / benzoyl-CoA / bos taurus / bovine / GNAT | ||||||
Function / homology | ![]() glycine N-acyltransferase / glycine N-benzoyltransferase / glycine N-acyltransferase activity / glycine N-benzoyltransferase activity / glycine metabolic process / monocarboxylic acid metabolic process / response to toxic substance / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Opperman, D.J. / Ebrecht, A.C. / Read, R.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of glycine N-acyltransferase clarifies its catalytic mechanism Authors: Ebrecht, A.C. / Badenhorst, C.P.S. / Read, R.J. / Opperman, D.J. / van Dijk, A.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.3 KB | Display | ![]() |
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PDB format | ![]() | 105 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.2 KB | Display | ![]() |
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Full document | ![]() | 443.1 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 36.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pk0C ![]() 7pk2C C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 33999.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q2KIR7, glycine N-acyltransferase, glycine N-benzoyltransferase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.69 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 1.5 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→48.09 Å / Num. obs: 87439 / % possible obs: 97.79 % / Redundancy: 8.6 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.015 / Rrim(I) all: 0.046 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.66→1.69 Å / Num. unique obs: 2764 / CC1/2: 0.3 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.65→48.09 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.989 / SU ML: 0.064 / SU R Cruickshank DPI: 0.0819 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.22 Å2 / Biso mean: 34.4887 Å2 / Biso min: 18.29 Å2
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Refinement step | Cycle: final / Resolution: 1.65→48.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.654→1.697 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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