+Open data
-Basic information
Entry | Database: PDB / ID: 2vx7 | |||||||||
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Title | CELLVIBRIO JAPONICUS MANNANASE CJMAN26C MANNOBIOSE-BOUND FORM | |||||||||
Components | CELLVIBRIO JAPONICUS MANNANASE CJMAN26C | |||||||||
Keywords | HYDROLASE / CELLVIBRIO JAPONICUS / MANNANASE / CJMAN26C | |||||||||
Function / homology | Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 4beta-beta-mannobiose Function and homology information | |||||||||
Biological species | CELLVIBRIO JAPONICUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Cartmell, A. / Topakas, E. / Ducros, V.M.-A. / Suits, M.D.L. / Davies, G.J. / Gilbert, H.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: The Cellvibrio Japonicus Mannanase Cjman26C Displays a Unique Exo-Mode of Action that is Conferred by Subtle Changes to the Distal Region of the Active Site. Authors: Cartmell, A. / Topakas, E. / Ducros, V.M.-A. / Suits, M.D.L. / Davies, G.J. / Gilbert, H.J. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vx7.cif.gz | 170.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vx7.ent.gz | 132.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vx7_validation.pdf.gz | 794.8 KB | Display | wwPDB validaton report |
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Full document | 2vx7_full_validation.pdf.gz | 794.6 KB | Display | |
Data in XML | 2vx7_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 2vx7_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/2vx7 ftp://data.pdbj.org/pub/pdb/validation_reports/vx/2vx7 | HTTPS FTP |
-Related structure data
Related structure data | 2vx4C 2vx5C 2vx6C 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: 44327.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-beta-D-mannopyranose / 4beta-beta-mannobiose |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Sequence details | STARTING RESIDUE IS LEU 53. GLU 338 WAS MUTATED TO AN ALANINE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.14 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 48533 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J9Y Resolution: 1.8→19.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.429 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.562 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.94 Å
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