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- PDB-5v0z: Crystal structure of Galactoside O-acetyltransferase complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5v0z | ||||||
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Title | Crystal structure of Galactoside O-acetyltransferase complex with CoA (P32 space group). | ||||||
![]() | Putative acetyltransferase SACOL2570 | ||||||
![]() | TRANSFERASE / Structural Genomics / CSGID / acetyltransferase / Coenzyme-A / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | ![]() galactoside O-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Czub, M.P. / Porebski, P.J. / Knapik, A.A. / Niedzialkowska, E. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Galactoside O-acetyltransferase complex with CoA (P32 space group). Authors: Czub, M.P. / Porebski, P.J. / Knapik, A.A. / Niedzialkowska, E. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 292.5 KB | Display | ![]() |
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PDB format | ![]() | 235.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 34.8 KB | Display | |
Data in CIF | ![]() | 52.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5u2kS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 22417.127 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: COL / Gene: SACOL2570 / Plasmid: pMCSG7 / Production host: ![]() ![]() References: UniProt: Q5HCZ5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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-Non-polymers , 6 types, 871 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-UNX / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.96 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 1uL of 15 mg/ml protein incubated with 5mM CoA were mixed with 1 uL of 25% w/v PEG 3350, 250 mM Sodium/Potassium phosphate, 30% v/v Ethylene glycol and equilibrated against well solution in ...Details: 1uL of 15 mg/ml protein incubated with 5mM CoA were mixed with 1 uL of 25% w/v PEG 3350, 250 mM Sodium/Potassium phosphate, 30% v/v Ethylene glycol and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 23, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.26→50 Å / Num. obs: 159888 / % possible obs: 99.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.027 / Rrim(I) all: 0.048 / Χ2: 0.606 / Net I/σ(I): 6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5U2K Resolution: 1.26→50 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / SU B: 1.505 / SU ML: 0.028 / SU R Cruickshank DPI: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.041 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.91 Å2 / Biso mean: 19.58 Å2 / Biso min: 6.18 Å2
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Refinement step | Cycle: final / Resolution: 1.26→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.26→1.293 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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