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Open data
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Basic information
Entry | Database: PDB / ID: 8bgn | ||||||
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Title | N,N-diacetylchitobiose deacetylase from Pyrococcus chitonophagus | ||||||
![]() | Diacetylchitobiose deacetylase | ||||||
![]() | HYDROLASE / hyperthermophile | ||||||
Function / homology | N-acetylglucosaminylphosphatidylinositol deacetylase activity / N-acetylglucosaminyl phosphatidylinositol deacetylase-related / Putative deacetylase LmbE-like domain superfamily / GlcNAc-PI de-N-acetylase / GPI anchor biosynthetic process / metal ion binding / Diacetylchitobiose deacetylase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rypniewski, W. / Bejger, M. / Biniek-Antosiak, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural, Thermodynamic and Enzymatic Characterization of N , N -Diacetylchitobiose Deacetylase from Pyrococcus chitonophagus. Authors: Biniek-Antosiak, K. / Bejger, M. / Sliwiak, J. / Baranowski, D. / Mohammed, A.S.A. / Svergun, D.I. / Rypniewski, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.3 KB | Display | ![]() |
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PDB format | ![]() | 137.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8bgoC ![]() 8bgpC ![]() 4xm0S C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 2 - 267 / Label seq-ID: 2 - 267
NCS ensembles :
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Components
#1: Protein | Mass: 30971.605 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.88 % |
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Crystal grow | Temperature: 308 K / Method: vapor diffusion, hanging drop Details: 0.1M HEPES, pH7.5, 2% v/v PEG 400, 2.0M ammonium sulfate |
-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: Nov 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→49.3 Å / Num. obs: 24234 / % possible obs: 99.08 % / Redundancy: 19.4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.76→2.86 Å / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2190 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XM0 Resolution: 2.76→49.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 14.411 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.341 / 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: 156.84 Å2 / Biso mean: 72.754 Å2 / Biso min: 38.83 Å2
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Refinement step | Cycle: final / Resolution: 2.76→49.3 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.763→2.835 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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