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- PDB-5xsx: Crystal structure of an archaeal chitinase in the substrate-compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xsx | |||||||||
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Title | Crystal structure of an archaeal chitinase in the substrate-complex form (P212121) | |||||||||
![]() | Chitinase | |||||||||
![]() | HYDROLASE / chitinase | |||||||||
Function / homology | ![]() chitinase / chitinase activity / polysaccharide binding / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nishitani, Y. / Miki, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of an archaeal chitinase ChiD and its ligand complexes. Authors: Nishitani, Y. / Horiuchi, A. / Aslam, M. / Kanai, T. / Atomi, H. / Miki, 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 | ![]() | 213.6 KB | Display | ![]() |
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PDB format | ![]() | 170.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1017.5 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 49.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xsvC ![]() 5xswSC 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: 56160.203 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 321-805 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris-HCl (pH 8.5), NH4H2PO4 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 50103 / % possible obs: 100 % / Redundancy: 13.1 % / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.65→2.71 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XSW Resolution: 2.642→49.626 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.642→49.626 Å
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Refine LS restraints |
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LS refinement shell |
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