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Open data
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Basic information
Entry | Database: PDB / ID: 1itx | ||||||
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Title | Catalytic Domain of Chitinase A1 from Bacillus circulans WL-12 | ||||||
![]() | Glycosyl Hydrolase | ||||||
![]() | HYDROLASE / Alpha-Beta (TIM) Barrel | ||||||
Function / homology | ![]() chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / carbohydrate binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Iwahori, F. / Matsumoto, T. / Watanabe, T. / Nonaka, T. | ||||||
![]() | Journal: PROC.JPN.ACAD.,SER.B / Year: 1999 Title: Three-dimensional structure of the catalytic domain of chitinase A1 from Bacillus circulans WL-12 at a very high resolution Authors: Matsumoto, T. / Nonaka, T. / Hashimoto, M. / Watanabe, T. / Mitsui, Y. #1: ![]() Title: Trp122 and Trp134 on the surface of the catalytic domain are essential for crystalline chitin hydrolysis by Bacillus circulans chitinase A1 Authors: Watanabe, T. / Ishibashi, A. / Ariga, Y. / Hashimoto, M. / Nikaidou, N. / Sugiyama, J. / Matsumoto, T. / Nonaka, T. #2: ![]() Title: Crystallization and A Preliminary Crystallographic Analysis of the Catalytic Domain of Chitinase Al from Bacillus Circulans WL-12 Authors: Matsumoto, T. / Nonaka, T. / Katouda, H. / Hashimoto, M. / Watanabe, T. / Mitsui, Y. #3: ![]() Title: Identification of glutamic acid 204 and aspartic acid 200 in chitinase A1 of Bacillus circulans WL-12 as essential residues for chitinase activity Authors: Watanabe, T. / Kobori, K. / Miyashita, K. / Fujii, T. / Sakai, H. / Uchida, M. / Tanaka, H. #4: ![]() Title: Gene cloning of chitinase A1 from Bacillus circulans WL-12 revealed its evolutionary relationship to Serratia chitinase and to the type III homology units of fibronectin Authors: Watanabe, T. / Suzuki, K. / Oyanagi, W. / Ohnishi, K. / Tanaka, H. #5: ![]() Title: Roles of the exposed aromatic residues in crystalline chitin hydrolysis by chitinase A from Serratia marcescens 2170 Authors: Uchiyama, T. / Katouno, f. / Nikaidou, N. / Nonaka, T. / Sugiyama, J. / Watanabe, 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 | ![]() | 216.6 KB | Display | ![]() |
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PDB format | ![]() | 170.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.6 KB | Display | ![]() |
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Full document | ![]() | 444.6 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 42.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ctnS 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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Unit cell |
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Components
#1: Protein | Mass: 45529.199 Da / Num. of mol.: 1 / Fragment: Catalytic Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: PEG 4000, potassium dihydrophosphate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 18, 2001 |
Radiation | Monochromator: undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.5 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→36.793 Å / Num. all: 139823 / Num. obs: 139823 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 5.943 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.1→1.13 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.4 / Num. unique all: 10242 / Rsym value: 0.248 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CTN Resolution: 1.1→36.793 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Some waters are listed as disorders coupled with some parts of the protein molecules.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.354 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→36.793 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.129 Å / Total num. of bins used: 20
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