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- PDB-4cd4: The structure of GH26 beta-mannanase CjMan26C from Cellvibrio jap... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cd4 | ||||||
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Title | The structure of GH26 beta-mannanase CjMan26C from Cellvibrio japonicus in complex with ManIFG | ||||||
![]() | ENDO-1,4-BETA MANNANASE, PUTATIVE, MAN26C | ||||||
![]() | HYDROLASE / BETA-MANNOSIDASE / MANNOSIDASE / GLYCOSIDE HYDROLASE / GH26 / GH113 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / MANNOSE / GLYCOSIDASE INHIBITION / QUANTUM MECHANICS / BIOCATALYSIS / CONFORMATION | ||||||
Function / homology | ![]() substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Williams, R.J. / Iglesias-Fernandez, J. / Stepper, J. / Jackson, A. / Thompson, A.J. / Lowe, E.C. / White, J.M. / Gilbert, H.J. / Rovira, C. / Davies, G.J. / Williams, S.J. | ||||||
![]() | ![]() Title: Combined Inhibitor Free-Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate. Authors: Williams, R.J. / Iglesias-Fernandez, J. / Stepper, J. / Jackson, A. / Thompson, A.J. / Lowe, E.C. / White, J.M. / Gilbert, H.J. / Rovira, C. / Davies, G.J. / Williams, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.9 KB | Display | ![]() |
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PDB format | ![]() | 156.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.4 KB | Display | ![]() |
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Full document | ![]() | 454 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 38.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cd5C ![]() 4cd6C ![]() 4cd7C ![]() 4cd8C ![]() 2vx7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46606.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B3PGI1, mannan endo-1,4-beta-mannosidase | ||||||
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#2: Chemical | #3: Sugar | ChemComp-BMA / | #4: Chemical | ChemComp-IFM / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 5.6 / Details: 100 MM SODIUM CITRATE PH 5.6, 15% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→54.46 Å / Num. obs: 142150 / % possible obs: 88.8 % / Observed criterion σ(I): 2 / Redundancy: 14.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 0.8 / % possible all: 20.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VX7 Resolution: 1.2→73.19 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.85 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / 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: 15.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→73.19 Å
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Refine LS restraints |
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