+Open data
-Basic information
Entry | Database: PDB / ID: 9k72 | ||||||
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Title | Crystal structure of TsaBgl using merged datasets | ||||||
Components | beta-glucosidase | ||||||
Keywords | HYDROLASE / beta-glucosidase | ||||||
Function / homology | Function and homology information : / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol Similarity search - Function | ||||||
Biological species | Thermoanaerobacterium saccharolyticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Nam, K.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Crystal structure of TsaBgl using merged datasets Authors: Nam, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9k72.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9k72.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 9k72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9k72_validation.pdf.gz | 438.5 KB | Display | wwPDB validaton report |
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Full document | 9k72_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 9k72_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 9k72_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/9k72 ftp://data.pdbj.org/pub/pdb/validation_reports/k7/9k72 | HTTPS FTP |
-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
#1: Protein | Mass: 51791.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacterium saccharolyticum (bacteria) Gene: Tsac_2208 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3VXG7, beta-glucosidase | ||||||
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#2: Chemical | ChemComp-TRS / | ||||||
#3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.78 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Tris-HCl, PEG4000, MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→100 Å / Num. obs: 67418 / % possible obs: 99.32 % / Redundancy: 14.3 % / CC1/2: 0.8547 / Net I/σ(I): 3.42 |
Reflection shell | Resolution: 1.55→1.6 Å / Num. unique obs: 7112 / CC1/2: 0.2974 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→57.86 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→57.86 Å
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Refine LS restraints |
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LS refinement shell |
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