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Yorodumi- PDB-7vt5: Crystal structure of CBM deleted MtGlu5 from Meiothermus taiwanen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vt5 | ||||||
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Title | Crystal structure of CBM deleted MtGlu5 from Meiothermus taiwanensis WR-220 | ||||||
Components | Endoglucanase H | ||||||
Keywords | HYDROLASE / cellulase / GH5 / Meiothermus taiwanensis WR-220 / endo-beta-1 / 4-glucanase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Meiothermus taiwanensis WR-220 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Ye, T.J. / Ko, P.T. / Huang, K.F. / Wu, S.H. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: Synergic action of an inserted carbohydrate-binding module in a glycoside hydrolase family 5 endoglucanase. Authors: Ye, T.J. / Huang, K.F. / Ko, T.P. / Wu, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vt5.cif.gz | 183.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vt5.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 7vt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/7vt5 ftp://data.pdbj.org/pub/pdb/validation_reports/vt/7vt5 | HTTPS FTP |
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-Related structure data
Related structure data | 7vt4C 7vt6C 7vt7C 7vt8C 3mmuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39168.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CBM deleted MtGlu5 Source: (gene. exp.) Meiothermus taiwanensis WR-220 (bacteria) Production host: Escherichia coli B (bacteria) / References: UniProt: A0A399DY85, cellulase |
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#2: Chemical | ChemComp-TRP / |
#3: Chemical | ChemComp-MET / |
#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: 2.09 Å3/Da / Density % sol: 37.17 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / Details: 20mM Tris, 100mM NaCl, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→50 Å / Num. obs: 51808 / % possible obs: 96 % / Redundancy: 3.7 % / Biso Wilson estimate: 13.34 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.034 / Χ2: 1.435 / Net I/σ(I): 26.14 |
Reflection shell | Resolution: 1.46→1.51 Å / Rmerge(I) obs: 0.503 / Num. unique obs: 4780 / CC1/2: 0.856 / Rpim(I) all: 0.32 / Rrim(I) all: 0.6 / Χ2: 1.156 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3mmu Resolution: 1.46→24.22 Å / SU ML: 0.1268 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6343 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: 21.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→24.22 Å
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Refine LS restraints |
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LS refinement shell |
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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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