+Open data
-Basic information
Entry | Database: PDB / ID: 7vt6 | ||||||
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Title | Crystal structure of CBM deleted MtGlu5 in complex with BGC. | ||||||
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: 1.53 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 | 7vt6.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vt6.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 7vt6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/7vt6 ftp://data.pdbj.org/pub/pdb/validation_reports/vt/7vt6 | HTTPS FTP |
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-Related structure data
Related structure data | 7vt4C 7vt5C 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: Sugar | ChemComp-BGC / | ||||||
#3: Chemical | #4: Chemical | ChemComp-TRP / | #5: 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: 2.13 Å3/Da / Density % sol: 38.23 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / Details: 20 mM Tris, 100 mM 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: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 45521 / % possible obs: 94.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 13.65 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.031 / Rrim(I) all: 0.062 / Χ2: 1.369 / Net I/σ(I): 33.82 |
Reflection shell | Resolution: 1.53→1.58 Å / Rmerge(I) obs: 0.186 / Num. unique obs: 4725 / CC1/2: 0.975 / Rpim(I) all: 0.097 / Rrim(I) all: 0.21 / Χ2: 0.684 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3mmu Resolution: 1.53→24.28 Å / SU ML: 0.1199 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.9853 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: 18.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→24.28 Å
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Refine LS restraints |
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LS refinement shell |
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