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Yorodumi- PDB-2bvy: The structure and characterization of a modular endo-beta-1,4-man... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bvy | ||||||
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Title | The structure and characterization of a modular endo-beta-1,4-mannanase from Cellulomonas fimi | ||||||
Components | BETA-1,4-MANNANASE | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / BETA-1 / 4-MANNANASE / FAMILY 26 / CLAN GH-A / CELLULOMONAS FIMI | ||||||
Function / homology | Function and homology information substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase activity / cellulase activity / cellulose catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | CELLULOMONAS FIMI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Le Nours, J. / Anderson, L. / Stoll, D. / Stalbrand, H. / Lo Leggio, L. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: The Structure and Characterization of a Modular Endo-Beta-1,4-Mannanase from Cellulomonas Fimi Authors: Le Nours, J. / Anderson, L. / Stoll, D. / Stalbrand, H. / Lo Leggio, L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bvy.cif.gz | 99.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bvy.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 2bvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bvy_validation.pdf.gz | 466 KB | Display | wwPDB validaton report |
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Full document | 2bvy_full_validation.pdf.gz | 472.5 KB | Display | |
Data in XML | 2bvy_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 2bvy_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/2bvy ftp://data.pdbj.org/pub/pdb/validation_reports/bv/2bvy | HTTPS FTP |
-Related structure data
Related structure data | 2bvtC 1j9yS 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: 50456.098 Da / Num. of mol.: 1 / Fragment: RESIDUES 52-514 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CELLULOMONAS FIMI (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9XCV5, mannan endo-1,4-beta-mannosidase | ||||
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#2: Chemical | ChemComp-CAC / | ||||
#3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.65 % |
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Crystal grow | pH: 6.5 Details: 30% W/V PEG8000 0.1M SODIUM CACODYLATE PH 6.5 0.2M SODIUM ACETATE TRIHYDRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97935 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 5, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 28207 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.25→2.33 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.8 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J9Y Resolution: 2.25→29.65 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 557694.21 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.4002 Å2 / ksol: 0.38181 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→29.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
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Xplor file |
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