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Yorodumi- PDB-3wl4: N,N'-diacetylchitobiose deacetylase (Se-derivative) from Pyrococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wl4 | ||||||
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Title | N,N'-diacetylchitobiose deacetylase (Se-derivative) from Pyrococcus furiosus | ||||||
Components | Uncharacterized protein | ||||||
Keywords | HYDROLASE / Zn-dependent deacetylase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.54 Å | ||||||
Authors | Nakamura, T. / Niiyama, M. / Hashimoto, W. / Uegaki, K. | ||||||
Citation | Journal: Febs J. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wl4.cif.gz | 131.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wl4.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/3wl4 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/3wl4 | HTTPS FTP |
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-Related structure data
-Links
-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.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0354 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U3V1 |
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-Non-polymers , 7 types, 362 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.99522, 0.97910, 0.97949 | ||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.54→26.4 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.814 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.05 / 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: 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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