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- PDB-4xlz: N,N'-diacetylchitobiose deacetylase (SeMet derivative) from Pyroc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xlz | ||||||
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Title | N,N'-diacetylchitobiose deacetylase (SeMet derivative) from Pyrococcus furiosus in the presence of cadmium | ||||||
![]() | Uncharacterized protein | ||||||
![]() | METAL BINDING PROTEIN / CE-14 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. / Ida, K. / Uegaki, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Multiple crystal forms of N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus. Authors: Nakamura, T. / Niiyama, M. / Hashimoto, W. / Ida, K. / Abe, M. / Morita, J. / Uegaki, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 386.2 KB | Display | ![]() |
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PDB format | ![]() | 312.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 517.7 KB | Display | ![]() |
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Full document | ![]() | 584.5 KB | Display | |
Data in XML | ![]() | 85.2 KB | Display | |
Data in CIF | ![]() | 117.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xm0C ![]() 4xm1C ![]() 4xm2C ![]() 3wl4S C: citing same article ( S: Starting model for refinement |
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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 , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 31392.840 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1507 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-HEZ / #4: Chemical | ChemComp-TRS / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl (pH 8.0), 0.2M MgCl2, 3.0M 1,6-hexanediol, 5mM CdCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99522 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→50 Å / Num. obs: 435340 / % possible obs: 95.2 % / Redundancy: 1.9 % / Net I/σ(I): 15.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WL4 Resolution: 1.51→31.16 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.222 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→31.16 Å
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Refine LS restraints |
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