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Yorodumi- PDB-6d2w: Crystal structure of Prevotella bryantii endo-beta-mannanase/endo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d2w | ||||||
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Title | Crystal structure of Prevotella bryantii endo-beta-mannanase/endo-beta-glucanase PbGH26A-GH5A | ||||||
Components | Aryl-phospho-beta-D-glucosidase BglC, GH1 family | ||||||
Keywords | HYDROLASE / glycosyl hydrolase family 26 / glycosyl hydrolase family 5 / GH26 / GH5 / mannanase / glucanase / polysaccharide utilization locus / Prevotella bryantii | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Prevotella bryantii B14 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Stogios, P.J. / Skarina, T. / McGregor, N. / Nocek, B. / Di Leo, R. / Brumer, H. / Savchenko, A. | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Prevotella bryantii endo-beta-mannanase/endo-beta-glucanase PbGH26A-GH5A Authors: McGregor, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d2w.cif.gz | 590.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d2w.ent.gz | 482.5 KB | Display | PDB format |
PDBx/mmJSON format | 6d2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6d2w_validation.pdf.gz | 465.7 KB | Display | wwPDB validaton report |
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Full document | 6d2w_full_validation.pdf.gz | 473.2 KB | Display | |
Data in XML | 6d2w_validation.xml.gz | 66.6 KB | Display | |
Data in CIF | 6d2w_validation.cif.gz | 102.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/6d2w ftp://data.pdbj.org/pub/pdb/validation_reports/d2/6d2w | HTTPS FTP |
-Related 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: 86998.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prevotella bryantii B14 (bacteria) / Gene: PBR_0368, SAMN05444375_1266 / Plasmid: p15Tv-lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Gold / References: UniProt: D8DY19 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.06 Å3/Da / Density % sol: 40.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 1.6 M ammonium sulfate, 12% glycerol, 20 mg/mL protein. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97914 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 80833 / % possible obs: 98.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.069 / Net I/σ(I): 9.89 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 3908 / CC1/2: 0.583 / Rpim(I) all: 0.444 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WDQ, 3VDH Resolution: 2.1→19.812 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→19.812 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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