+Open data
-Basic information
Entry | Database: PDB / ID: 2vx6 | |||||||||
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Title | CELLVIBRIO JAPONICUS MANNANASE CJMAN26C Gal1Man4-BOUND FORM | |||||||||
Components | CELLVIBRIO JAPONICUS MANNANASE CJMAN26C | |||||||||
Keywords | HYDROLASE / MANNO- OLIGOSACCHARIDE / GAL1MAN4 / CJMAN26C / MANNANASE / CELLVIBRIO JAPONICUS | |||||||||
Function / homology | Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta Function and homology information | |||||||||
Biological species | CELLVIBRIO JAPONICUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 | 2vx6.cif.gz | 197.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vx6.ent.gz | 155.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/2vx6 ftp://data.pdbj.org/pub/pdb/validation_reports/vx/2vx6 | HTTPS FTP |
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-Related structure data
Related structure data | 2vx4C 2vx5C 2vx7C 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: 44385.266 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)-[alpha-D-galactopyranose-(1-6)]beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-[alpha-D-galactopyranose-(1-6)]beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose Source method: isolated from a genetically manipulated source | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | GALACTOSE (GAL): GALACTOSE IS PART OF A PENTASACCHARIDE GAL-MAN4 MANNOSE (MAN): THE FOUR MANNOSE ...GALACTOSE (GAL): GALACTOSE IS PART OF A PENTASACCH | Sequence details | STARTING RESIDUE IS LEU 53 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 59.37 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0712 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0712 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→20 Å / Num. obs: 72691 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 38.4 |
Reflection shell | Resolution: 1.57→1.63 Å / Redundancy: 11 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 10.4 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J9Y Resolution: 1.57→10.53 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.479 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.051 / 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: 9.167 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→10.53 Å
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