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Yorodumi- PDB-7q6y: The X-ray crystal structure of CbTan2, a tannase enzyme from Clos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q6y | ||||||||||||
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Title | The X-ray crystal structure of CbTan2, a tannase enzyme from Clostridium butyricum | ||||||||||||
Components | Alpha/beta hydrolaseAlpha/beta hydrolase superfamily | ||||||||||||
Keywords | HYDROLASE / Tannase / Serine hydrolase / Gallate / Tannic acid | ||||||||||||
Function / homology | Alpha/Beta hydrolase fold / hydrolase activity / DI(HYDROXYETHYL)ETHER / Alpha/beta hydrolase Function and homology information | ||||||||||||
Biological species | Clostridium butyricum (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||||||||
Authors | Coleman, T. / Mazurkewich, S. / Larsbrink, J. | ||||||||||||
Funding support | Sweden, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Structural diversity and substrate preferences of three tannase enzymes encoded by the anaerobic bacterium Clostridium butyricum. Authors: Ristinmaa, A.S. / Coleman, T. / Cesar, L. / Langborg Weinmann, A. / Mazurkewich, S. / Branden, G. / Hasani, M. / Larsbrink, J. #1: Journal: J.Biol.Chem. / Year: 2022 Title: The X-ray crystal structure of CbTan2, a tannase enzyme from Clostridium butyricum Authors: Coleman, T. / Mazurkewich, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q6y.cif.gz | 198 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q6y.ent.gz | 157.7 KB | Display | PDB format |
PDBx/mmJSON format | 7q6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/7q6y ftp://data.pdbj.org/pub/pdb/validation_reports/q6/7q6y | HTTPS FTP |
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-Related structure data
Related structure data | 4j0cS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 54966.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium butyricum (bacteria) / Gene: CBLFYP62_01769, FF104_18625 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6M0U600 #2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.58 Å3/Da / Density % sol: 52.28 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2 M calcium chloride dihydrate 0.1 M sodium acetate, pH 5.0 20 % PEG 6,000 25 mg/mL protein PH range: 4.75-5.75 / Temp details: 25 C |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→46.45 Å / Num. obs: 56815 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 43.04 Å2 / Rmerge(I) obs: 0.196 / Net I/σ(I): 11.93 |
Reflection shell | Resolution: 2.22→2.3 Å / Redundancy: 13.5 % / Rmerge(I) obs: 2.463 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5560 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J0C Resolution: 2.22→46.45 Å / SU ML: 0.334 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.825 Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→46.45 Å
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Refine LS restraints |
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LS refinement shell |
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