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- PDB-4d4a: Structure of the catalytic domain (BcGH76) of the Bacillus circul... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4d4a | ||||||
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Title | Structure of the catalytic domain (BcGH76) of the Bacillus circulans GH76 alpha mannanase, Aman6. | ||||||
![]() | ALPHA-1,6-MANNANASE | ||||||
![]() | HYDROLASE / GLYCOSIDE HYDROLASE / GH76 / CAZY / MANNAN / ENZYME-CARBOHYDRATE INTERACTION / GLYCOSIDASE INHIBITION / QUANTUM MECHANICS / TRANSITION STATE | ||||||
Function / homology | ![]() catalytic activity / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 324.5 KB | Display | ![]() |
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PDB format | ![]() | 263.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.4 KB | Display | ![]() |
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Full document | ![]() | 460.7 KB | Display | |
Data in XML | ![]() | 35.7 KB | Display | |
Data in CIF | ![]() | 56.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d4bC ![]() 4d4cC ![]() 4d4dC ![]() 5agdC ![]() 3k7xS 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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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.) ![]() ![]() ![]() References: UniProt: Q9Z4P9, mannan endo-1,6-alpha-mannosidase #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.8 % / 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→43.8 Å / Num. obs: 141868 / % possible obs: 98.4 % / Observed criterion σ(I): -3.7 / Redundancy: 8.3 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 1.7 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3K7X Resolution: 1.4→65.49 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.037 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.048 / 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: 20.257 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→65.49 Å
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Refine LS restraints |
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