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- PDB-6sk1: Diaminobutyrate acetyltransferase EctA from Paenibacillus lautus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sk1 | |||||||||
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Title | Diaminobutyrate acetyltransferase EctA from Paenibacillus lautus in complex with coenzyme A | |||||||||
![]() | L-2,4-diaminobutyric acid acetyltransferase | |||||||||
![]() | TRANSFERASE / L-2 / 4-diaminobutyrate acetyltransferase / acetyl coenzyme A / acetylation / stress response / chemical chaperone | |||||||||
Function / homology | ![]() diaminobutyrate acetyltransferase / diaminobutyrate acetyltransferase activity / ectoine biosynthetic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Richter, A.A. / Kobus, S. / Czech, L. / Hoeppner, A. / Bremer, E. / Smits, S.H.J. | |||||||||
![]() | ![]() Title: The architecture of the diaminobutyrate acetyltransferase active site provides mechanistic insight into the biosynthesis of the chemical chaperone ectoine. Authors: Richter, A.A. / Kobus, S. / Czech, L. / Hoeppner, A. / Zarzycki, J. / Erb, T.J. / Lauterbach, L. / Dickschat, J.S. / Bremer, E. / Smits, S.H.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.9 KB | Display | ![]() |
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PDB format | ![]() | 38.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 609.2 KB | Display | ![]() |
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Full document | ![]() | 614.5 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6sjyC ![]() 6sl8C ![]() 6slkSC ![]() 6sllC 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: 20827.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Y412MC10 / Gene: ectA, GYMC10_5665 / Production host: ![]() ![]() References: UniProt: D3EKC1, diaminobutyrate acetyltransferase |
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#2: Chemical | ChemComp-COA / |
#3: Chemical | ChemComp-ACT / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop Details: 0.1 M magnesium chloride, 0.1 M sodium chloride, 12 % (w/v) PEG 4000, 0.1 M tri-sodium citrate pH 5.5, 5 mM coenzyme A |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→51.89 Å / Num. obs: 70942 / % possible obs: 99.9 % / Redundancy: 8.3 % / Rsym value: 0.067 / Net I/σ(I): 13.46 |
Reflection shell | Resolution: 1.13→1.21 Å / Num. unique obs: 12931 / Rsym value: 1.343 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6SLK Resolution: 1.5→51.88 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.904 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.065 / 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: 68.23 Å2 / Biso mean: 14.566 Å2 / Biso min: 5.33 Å2
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Refinement step | Cycle: final / Resolution: 1.5→51.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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