+Open data
-Basic information
Entry | Database: PDB / ID: 8oug | ||||||
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Title | Exo-beta-d-glucosaminidase from Pyrococcus chitonophagus | ||||||
Components | Beta-galactosidase | ||||||
Keywords | HYDROLASE / hyperthermophile | ||||||
Function / homology | Function and homology information beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Thermococcus chitonophagus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Rypniewski, W. / Biniek-Antosiak, K. / Bejger, M. | ||||||
Funding support | Poland, 1items
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Citation | Journal: To Be Published Title: Exo-beta-d-glucosaminidase from Pyrococcus chitonophagus Authors: Rypniewski, W. / Biniek-Antosiak, K. / Bejger, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oug.cif.gz | 333.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oug.ent.gz | 272.4 KB | Display | PDB format |
PDBx/mmJSON format | 8oug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/8oug ftp://data.pdbj.org/pub/pdb/validation_reports/ou/8oug | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 91143.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus chitonophagus (archaea) / Gene: A3L04_10820 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A160VTD9 | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.92 % |
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Crystal grow | Temperature: 308 K / Method: vapor diffusion, sitting drop / Details: 0.1M SPG buffer pH 8.0, 25% v/v PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 46003 / % possible obs: 99.5 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 19.43 |
Reflection shell | Resolution: 2.1→2.23 Å / Num. unique obs: 7306 / CC1/2: 0.839 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.42 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.955 / SU B: 15.881 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 141.13 Å2 / Biso mean: 47.76 Å2 / Biso min: 32.22 Å2
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Refinement step | Cycle: final / Resolution: 2.1→46.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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