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Yorodumi- PDB-4cd5: The structure of GH26 beta-mannanase CjMan26C from Cellvibrio jap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cd5 | ||||||
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Title | The structure of GH26 beta-mannanase CjMan26C from Cellvibrio japonicus in complex with ManMIm | ||||||
Components | ENDO-1,4-BETA MANNANASE, PUTATIVE, MAN26C | ||||||
Keywords | HYDROLASE / BETA-MANNOSIDASE / MANNOSIDASE / GLYCOSIDE HYDROLASE / GH26 / GH113 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / MANNOSE / GLYCOSIDASE INHIBITION / QUANTUM MECHANICS / BIOCATALYSIS / CONFORMATION | ||||||
Function / homology | Function and homology information substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity Similarity search - Function | ||||||
Biological species | CELLVIBRIO JAPONICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
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. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 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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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 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 | 4cd5.cif.gz | 188.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cd5.ent.gz | 149.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cd5_validation.pdf.gz | 465.8 KB | Display | wwPDB validaton report |
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Full document | 4cd5_full_validation.pdf.gz | 467.5 KB | Display | |
Data in XML | 4cd5_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 4cd5_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/4cd5 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/4cd5 | HTTPS FTP |
-Related structure data
Related structure data | 4cd4C 4cd6C 4cd7C 4cd8C 2vx7S 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 on special symmetry positions |
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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.) CELLVIBRIO JAPONICUS (bacteria) / Strain: UEDA107 / Plasmid: PET20B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: B3PGI1, mannan endo-1,4-beta-mannosidase | ||||||
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#2: Chemical | #3: Sugar | ChemComp-BMA / | #4: Chemical | ChemComp-MVL / ( | #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: 2.81 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 5.6 / Details: 100MM SODIUM CITRATE PH 5.6, 15% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→32 Å / Num. obs: 208589 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 10 % / Mean I/σ(I) obs: 1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VX7 Resolution: 1.1→73.19 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.207 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / 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: 14.118 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→73.19 Å
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Refine LS restraints |
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