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- PDB-7dw8: Structure of a novel beta-mannanase BaMan113A with mannobiose, N2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dw8 | ||||||
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Title | Structure of a novel beta-mannanase BaMan113A with mannobiose, N236Y mutation. | ||||||
![]() | Endo-beta-1,4-mannanase | ||||||
![]() | HYDROLASE / Complex | ||||||
Function / homology | Glycoside hydrolase superfamily / 4beta-beta-mannobiose / Endo-beta-1,4-mannanase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, W.T. / Liu, W.D. / Zheng, Y.Y. | ||||||
![]() | ![]() Title: Functional and structural investigation of a novel beta-mannanase BaMan113A from Bacillus sp. N16-5. Authors: Liu, W. / Ma, C. / Liu, W. / Zheng, Y. / Chen, C.C. / Liang, A. / Luo, X. / Li, Z. / Ma, W. / Song, Y. / Guo, R.T. / Zhang, T. #1: ![]() Title: Functional and structural investigation of a Novel beta-Mannanase BaMan113B from Bacillus sp. N16-5 Authors: Liu, W.T. / Liu, W.D. / Zheng, Y.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161 KB | Display | ![]() |
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PDB format | ![]() | 123 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 32 KB | Display | |
Data in CIF | ![]() | 48.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dv7C ![]() 7dvjC ![]() 7dvzC ![]() 7dwaC ![]() 3civS S: Starting model for refinement C: citing same article ( |
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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: 40638.762 Da / Num. of mol.: 2 / Mutation: E142A, N236Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.77 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: tacsimate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. obs: 68892 / % possible obs: 93.5 % / Redundancy: 11.9 % / CC1/2: 0.871 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Num. unique obs: 6531 / CC1/2: 0.932 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CIV Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.976 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.119 / 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 max: 92.76 Å2 / Biso mean: 22.3 Å2 / Biso min: 12.4 Å2
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Refinement step | Cycle: final / Resolution: 1.9→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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