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Yorodumi- PDB-4d4c: The catalytic domain, BcGH76, of Bacillus circulans Aman6 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d4c | ||||||
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Title | The catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with 1,6-ManDMJ | ||||||
Components | ALPHA-1,6-MANNANASE | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / GH76 / CAZY / MANNAN / ENZYME-CARBOHYDRATE INTERACTION / GLYCOSIDASE INHIBITION / TRANSITION STATE | ||||||
Function / homology | Function and homology information catalytic activity / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | BACILLUS CIRCULANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Thompson, A.J. / Speciale, G. / Iglesias-Fernandez, J. / Hakki, Z. / Belz, T. / Cartmell, A. / Spears, R.J. / Stepper, J. / Gilbert, H.J. / Rovira, C. ...Thompson, A.J. / Speciale, G. / Iglesias-Fernandez, J. / Hakki, Z. / Belz, T. / Cartmell, A. / Spears, R.J. / Stepper, J. / Gilbert, H.J. / Rovira, C. / Williams, S.J. / Davies, G.J. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Evidence for a Boat Conformation at the Transition State of Gh76 Alpha-1,6-Mannanases- Key Enzymes in Bacterial and Fungal Mannoprotein Metabolism Authors: Thompson, A.J. / Speciale, G. / Iglesias-Fernandez, J. / Hakki, Z. / Belz, T. / Cartmell, A. / Spears, R.J. / Chandler, E. / Temple, M.J. / Stepper, J. / Gilbert, H.J. / Rovira, C. / ...Authors: Thompson, A.J. / Speciale, G. / Iglesias-Fernandez, J. / Hakki, Z. / Belz, T. / Cartmell, A. / Spears, R.J. / Chandler, E. / Temple, M.J. / Stepper, J. / Gilbert, H.J. / Rovira, C. / Williams, S.J. / Davies, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d4c.cif.gz | 308.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d4c.ent.gz | 250.4 KB | Display | PDB format |
PDBx/mmJSON format | 4d4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d4c_validation.pdf.gz | 483.2 KB | Display | wwPDB validaton report |
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Full document | 4d4c_full_validation.pdf.gz | 490.7 KB | Display | |
Data in XML | 4d4c_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 4d4c_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/4d4c ftp://data.pdbj.org/pub/pdb/validation_reports/d4/4d4c | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40930.859 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS CIRCULANS (bacteria) / Strain: TN31 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER References: UniProt: Q9Z4P9, mannan endo-1,6-alpha-mannosidase #2: Chemical | #3: Sugar | #4: Chemical | ChemComp-EDO / | #5: 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: 2.15 Å3/Da / Density % sol: 42.9 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1 M AMMONIUM NITRATE, PH 6.5, 20% PEG 3350 |
-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: May 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→43.3 Å / Num. obs: 173270 / % possible obs: 99.8 % / Observed criterion σ(I): -3.7 / Redundancy: 8 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 8 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PREVIOUSLY SOLVED NATIVE APO STRUCTURE Resolution: 1.3→65.06 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.97 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.054 / 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 |
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Refinement step | Cycle: LAST / Resolution: 1.3→65.06 Å
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Refine LS restraints |
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