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- PDB-3wl4: N,N'-diacetylchitobiose deacetylase (Se-derivative) from Pyrococc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wl4 | ||||||
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Title | N,N'-diacetylchitobiose deacetylase (Se-derivative) from Pyrococcus furiosus | ||||||
![]() | Uncharacterized protein | ||||||
![]() | HYDROLASE / Zn-dependent deacetylase | ||||||
Function / homology | ![]() N-acetylglucosaminylphosphatidylinositol deacetylase activity / GPI anchor biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakamura, T. / Niiyama, M. / Hashimoto, W. / Uegaki, K. | ||||||
![]() | ![]() Title: Expression from engineered Escherichia coli chromosome and crystallographic study of archaeal N,N'-diacetylchitobiose deacetylase Authors: Mine, S. / Niiyama, M. / Hashimoto, W. / Ikegami, T. / Koma, D. / Ohmoto, T. / Fukuda, Y. / Inoue, T. / Abe, Y. / Ueda, T. / Morita, J. / Uegaki, K. / Nakamura, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.8 KB | Display | ![]() |
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PDB format | ![]() | 110.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.4 KB | Display | ![]() |
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Full document | ![]() | 525.5 KB | Display | |
Data in XML | ![]() | 31.5 KB | Display | |
Data in CIF | ![]() | 42.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31392.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 362 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TAM.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/HE2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TAM.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/HE2.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-TAM / #6: Chemical | ChemComp-HEZ / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl (pH 8.0), 0.2M MgCl2, 3.4M 1,6-hexanediol, 5mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.54→50 Å / Num. all: 147090 / Num. obs: 143526 / % possible obs: 99.8 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 | ||||||||||||
Reflection shell | Resolution: 1.54→1.57 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.158 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→26.4 Å
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Refine LS restraints |
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