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Yorodumi- PDB-4uzn: The native structure of the family 46 carbohydrate-binding module... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uzn | ||||||
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Title | The native structure of the family 46 carbohydrate-binding module (CBM46) of endo-beta-1,4-glucanase B (Cel5B) from Bacillus halodurans | ||||||
Components | ENDO-BETA-1,4-GLUCANASE (CELULASE B) | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information organic substance metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding Similarity search - Function | ||||||
Biological species | BACILLUS HALODURANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Venditto, I. / Santos, H. / Ferreira, L.M.A. / Sakka, K. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Family 46 Carbohydrate-Binding Modules Contribute to the Enzymatic Hydrolysis of Xyloglucan and Beta-1,3-1,4-Glucans Through Distinct Mechanisms. Authors: Venditto, I. / Najmudin, S. / Luis, A.S. / Ferreira, L.M. / Sakka, K. / Knox, J.P. / Gilbert, H.J. / Fontes, C.M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2014 Title: Overproduction, Purification, Crystallization and Preliminary X-Ray Characterization of the Family 46 Carbohydrate-Binding Module (Cbm46) of Endo-Beta-1,4-Glucanase B (Celb) from Bacillus Halodurans. Authors: Venditto, I. / Santos, H. / Ferreira, L.M.A. / Sakka, K. / Fontes, C.M.G.A. / Najmudin, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uzn.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uzn.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 4uzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/4uzn ftp://data.pdbj.org/pub/pdb/validation_reports/uz/4uzn | HTTPS FTP |
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-Related structure data
Related structure data | 4uz8SC 4v2xC 4uzp S: Starting model for refinement C: citing same article (ref.) |
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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: 14326.695 Da / Num. of mol.: 2 Fragment: CARBOHYDRATE BINDING MODULE FAMILY 46, RESIDUES 457-653 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS HALODURANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9KF82 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.4-0.75 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE PROTEIN WAS COCRYSTALLISED WITH 10 MM OF 1,4-BETA-D-CELLOHEXAOSEIN 50 MM HEPES HCL PH 7.5, 200 MM NACL, 5 MM CACL2. 30%, V/V GLYCEROL ADDED ...Details: 0.4-0.75 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE PROTEIN WAS COCRYSTALLISED WITH 10 MM OF 1,4-BETA-D-CELLOHEXAOSEIN 50 MM HEPES HCL PH 7.5, 200 MM NACL, 5 MM CACL2. 30%, V/V GLYCEROL ADDED TO THE CRYSTALLIZATION BUFFER AS CRYOPROTECTANT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→44.37 Å / Num. obs: 10730 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.46→2.56 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UZ8 Resolution: 2.46→85.69 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 31.804 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 0.371 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. PDB_REDO WAS USED BEFORE THE ULTIMATE REFMAC5 REFINEMENT RUN.
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.816 Å2
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Refinement step | Cycle: LAST / Resolution: 2.46→85.69 Å
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Refine LS restraints |
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