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- PDB-6a8i: Crystal structure of endo-arabinanase ABN-TS D147N mutant in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6a8i | |||||||||
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Title | Crystal structure of endo-arabinanase ABN-TS D147N mutant in complex with arabinohexaose | |||||||||
![]() | endo-alpha-(1->5)-L-arabinanase | |||||||||
![]() | HYDROLASE / arabinanase / thermostable enzyme / glycoside hydrolase / gh43 | |||||||||
Function / homology | ![]() arabinan endo-1,5-alpha-L-arabinanase / arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yamaguchi, A. / Tada, T. | |||||||||
![]() | ![]() Title: Structures of endo-1,5-alpha-L-arabinanase mutants from Bacillus thermodenitrificans TS-3 in complex with arabino-oligosaccharides. Authors: Yamaguchi, A. / Sogabe, Y. / Fukuoka, S. / Sakai, T. / Tada, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.5 KB | Display | ![]() |
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PDB format | ![]() | 119.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 858 KB | Display | ![]() |
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Full document | ![]() | 869 KB | Display | |
Data in XML | ![]() | 30.8 KB | Display | |
Data in CIF | ![]() | 45.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6a8hC ![]() 1wl7S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36557.742 Da / Num. of mol.: 2 / Mutation: D147N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: abn-ts / Production host: ![]() ![]() References: UniProt: Q93HT9, arabinan endo-1,5-alpha-L-arabinanase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 16% PEG 8000, 0.2M magnesium chloride, 0.1M MES pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 51538 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.8 Å2 / Rpim(I) all: 0.055 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.6 % / Num. unique obs: 2522 / Rpim(I) all: 0.324 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WL7 Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.084 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 23.416 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→50 Å
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Refine LS restraints |
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