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- PDB-5kga: X-ray structure of a glucosamine N-Acetyltransferase from Clostri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kga | ||||||
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Title | X-ray structure of a glucosamine N-Acetyltransferase from Clostridium acetobutylicum, mutant D287N, in complex with N-acetylglucosamine | ||||||
![]() | Predicted acetyltransferase | ||||||
![]() | TRANSFERASE / N-aceryltransferase / acyltransferase / GNAT / tandem-GNAT | ||||||
Function / homology | acyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / COENZYME A / TETRAMETHYLAMMONIUM ION / Predicted acetyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dopkins, B.J. / Thoden, J.B. / Tipton, P.A. / Holden, H.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Studies on a Glucosamine/Glucosaminide N-Acetyltransferase. Authors: Dopkins, B.J. / Tipton, P.A. / Thoden, J.B. / Holden, H.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 | ![]() | 164.2 KB | Display | ![]() |
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PDB format | ![]() | 125.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 31.6 KB | Display | |
Data in CIF | ![]() | 46.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kf1SC ![]() 5kf2C ![]() 5kf8C ![]() 5kf9C ![]() 5kghC ![]() 5kgjC ![]() 5kgpC 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 4 molecules AB![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 38377.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Mutant D287N Source: (gene. exp.) ![]() Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 Gene: CA_C0184 / Production host: ![]() ![]() #2: Sugar | |
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-Non-polymers , 6 types, 584 molecules ![](data/chem/img/COA.gif)
![](data/chem/img/ACO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TMA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACO.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TMA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-TMA / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 8-11% PEG-8000, 100 mM homopipes, 5 mM CoA, 20 mM N-acetylglucosamine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Dec 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 54576 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 2.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.1 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5kf1 Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.543 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.047 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→50 Å
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Refine LS restraints |
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