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- PDB-3a4w: Crystal structures of catalytic site mutants of active domain 2 o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a4w | |||||||||
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Title | Crystal structures of catalytic site mutants of active domain 2 of thermostable chitinase from Pyrococcus furiosus complexed with chito-oligosaccharides | |||||||||
![]() | Chitinase | |||||||||
![]() | HYDROLASE / archaea / chitinase / glycosyl hydrolase | |||||||||
Function / homology | ![]() chitinase activity / chitin catabolic process / polysaccharide binding / chitin binding / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tsuji, H. / Nishimura, S. / Inui, T. / Ishikawa, K. / Nakamura, T. / Uegaki, K. | |||||||||
![]() | ![]() Title: Kinetic and crystallographic analyses of the catalytic domain of chitinase from Pyrococcus furiosus- the role of conserved residues in the active site Authors: Tsuji, H. / Nishimura, S. / Inui, T. / Kado, Y. / Ishikawa, K. / Nakamura, T. / Uegaki, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.5 KB | Display | ![]() |
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PDB format | ![]() | 107.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 37.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a4xC ![]() 3afbC ![]() 2dskS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34706.191 Da / Num. of mol.: 2 / Fragment: catalytic domain (AD), UNP residues 409-717 / Mutation: E526A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: VAPOR DIFFUSION, HANGING DROP, pH6.0, temperature 298K Temp details: 1.6M MgSO4 |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: Bruker DIP-6040 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 83345 |
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Processing
Software | Name: REFMAC / Version: 5.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DSK Resolution: 1.8→29.49 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.467 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.083 / 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: 10.401 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.798→1.845 Å / Total num. of bins used: 20
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