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Yorodumi- PDB-7bob: Exo-beta-1,4-mannosidase Op5Man5 from Opitutaceae bacterium strai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bob | ||||||
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Title | Exo-beta-1,4-mannosidase Op5Man5 from Opitutaceae bacterium strain TAV5 | ||||||
Components | Endo-beta-mannanase | ||||||
Keywords | HYDROLASE / Exo-beta-1 / 4-mannosidase / Termite hindgut / Reticulitermes flavipes / Glycosyl hydrolase family 5 / Verrucomicrobia / Opitutaceae | ||||||
Function / homology | : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Class I glutamine amidotransferase-like / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / Endo-beta-mannanase Function and homology information | ||||||
Biological species | Opitutaceae bacterium TAV5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kalyani, D.C. / Reichenbach, T. / Keskitalo, M.M. / Conrad, J. / Aspeborg, H. / Divne, C. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: J Struct Biol X / Year: 2021 Title: Crystal structure of a homotrimeric verrucomicrobial exo - beta -1,4-mannosidase active in the hindgut of the wood-feeding termite Reticulitermes flavipes . Authors: Kalyani, D.C. / Reichenbach, T. / Keskitalo, M.M. / Conrad, J. / Aspeborg, H. / Divne, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bob.cif.gz | 332.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bob.ent.gz | 270.2 KB | Display | PDB format |
PDBx/mmJSON format | 7bob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bob_validation.pdf.gz | 324.3 KB | Display | wwPDB validaton report |
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Full document | 7bob_full_validation.pdf.gz | 334.1 KB | Display | |
Data in XML | 7bob_validation.xml.gz | 56.2 KB | Display | |
Data in CIF | 7bob_validation.cif.gz | 78.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/7bob ftp://data.pdbj.org/pub/pdb/validation_reports/bo/7bob | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 67032.750 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: The following regions are flexible and not modeled: residues 213-221; residues 367-380, 588-601 Source: (gene. exp.) Opitutaceae bacterium TAV5 (bacteria) / Gene: OPIT5_10225 / Plasmid: pNIC-CH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -T1R / References: UniProt: W0J1H8 #2: 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: 3.47 Å3/Da / Density % sol: 64.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1 M phosphorus citrate (pH 4.2), 30 % (v/v) ethanol, and 5 % (w/v) polyethylene glycol 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.826561 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2017 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.826561 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.15 Å / Num. obs: 141664 / % possible obs: 99.7 % / Redundancy: 13.3 % / Biso Wilson estimate: 45.16 Å2 / CC1/2: 0.999 / Rsym value: 0.107 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 17459 / CC1/2: 0.768 / Rsym value: 1.865 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Cryo-EM model (3.7 A) Resolution: 2.2→48.867 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→48.867 Å
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Refine LS restraints |
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LS refinement shell |
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