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Yorodumi- PDB-6wqy: GH5-4 broad specificity endoglucanase from Bacteroides salanitronis -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wqy | |||||||||
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Title | GH5-4 broad specificity endoglucanase from Bacteroides salanitronis | |||||||||
Components | Cellulase | |||||||||
Keywords | HYDROLASE / Cellulase / xylanase / GH5 / endoglucanase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacteroides salanitronis | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | |||||||||
Authors | Bingman, C.A. / Smith, R.W. / Glasgow, E.M. / Fox, B.G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis. Authors: Glasgow, E.M. / Kemna, E.I. / Bingman, C.A. / Ing, N. / Deng, K. / Bianchetti, C.M. / Takasuka, T.E. / Northen, T.R. / Fox, B.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wqy.cif.gz | 235.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wqy.ent.gz | 191.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/6wqy ftp://data.pdbj.org/pub/pdb/validation_reports/wq/6wqy | HTTPS FTP |
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-Related structure data
Related structure data | 4im4C 6mq4C 6pz7C 6q1iC 6ui3C 6wqpC 6wqvC 6xrkC 6xsoC 6xsuC 4yheS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 42668.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides salanitronis (strain DSM 18170 / JCM 13567 / BL78) (bacteria) Strain: DSM 18170 / JCM 13567 / BL78 / Gene: Bacsa_0886 / Plasmid: pVP67K / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F0R2T3, cellulase | ||||||
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#2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 200 nL of a solution containing 59 mg/mL protein, 50 nM NaCl, 5 mM MOPS buffer pH 7 was mixed with 130 nL reservoir solution containing 16% PEG3350, 0.2 M MgCl2, and 0.1 M sodium acetate ...Details: 200 nL of a solution containing 59 mg/mL protein, 50 nM NaCl, 5 mM MOPS buffer pH 7 was mixed with 130 nL reservoir solution containing 16% PEG3350, 0.2 M MgCl2, and 0.1 M sodium acetate buffer at pH 5. Vapor diffusion in MRC plates. Crystals appeared within a few days, and were cryo-protected using a reservoir solution supplemented to 35% PEG3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.7749 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→29.24 Å / Num. obs: 165260 / % possible obs: 99.19 % / Redundancy: 12.1 % / Biso Wilson estimate: 11.23 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05084 / Rpim(I) all: 0.01479 / Rrim(I) all: 0.053 / Net I/σ(I): 22.62 |
Reflection shell | Resolution: 1.05→1.088 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.832 / Mean I/σ(I) obs: 1.68 / Num. unique obs: 15327 / CC1/2: 0.621 / Rpim(I) all: 0.3576 / Rrim(I) all: 0.9114 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4yhe Resolution: 1.05→29.24 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→29.24 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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