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- PDB-7akq: Structure of D169A/E171A double mutant of chitinase Chit42 from T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7akq | ||||||
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Title | Structure of D169A/E171A double mutant of chitinase Chit42 from Trichoderma harzianum complexed with chitintetraose obtained by soaking. | ||||||
![]() | Endochitinase 42 | ||||||
![]() | HYDROLASE / CHITINASE / HYDOLYTIC ENZYME / GLYCOSIL HYDROLASE / CHITIN / N-ACETYLGLUCOSAMINE / CHITINTETRAOSE / PREBIOTIC / OLIGOSACCARIDE / CHITOOLIGOSACCHARIDE / TRICHODERMA HARZIANUM. | ||||||
Function / homology | ![]() chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jimenez-Ortega, E. / Sanz-Aparicio, J. | ||||||
![]() | ![]() Title: Structural inspection and protein motions modelling of a fungal glycoside hydrolase family 18 chitinase by crystallography depicts a dynamic enzymatic mechanism Authors: Jimenez-Ortega, E. / Kidibule, P.E. / Fernandez-Lobato, M. / Sanz-Aparicio, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.8 KB | Display | ![]() |
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PDB format | ![]() | 71.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yljC ![]() 6yn4C ![]() 6epbS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45968.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 213 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ACT / | ||
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#5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % / Description: Bar |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 18% PEG 3000, 0.1M Zinc Acetate, 0.1 M Zn chloride, 0.1 M imidazole pH 8. Soaking experiment: Mother liquor supplemented with 2 mM EDTA and 30 mM chitintetraose. Cryoprotectant mother liquor ...Details: 18% PEG 3000, 0.1M Zinc Acetate, 0.1 M Zn chloride, 0.1 M imidazole pH 8. Soaking experiment: Mother liquor supplemented with 2 mM EDTA and 30 mM chitintetraose. Cryoprotectant mother liquor supplemented with 20% PEG 400. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2018 / Details: KB Mirrors |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→48.21 Å / Num. obs: 16652 / % possible obs: 90.1 % / Redundancy: 8.4 % / CC1/2: 0.987 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.064 / Rrim(I) all: 0.194 / Net I/av σ(I): 8.5 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.32→2.4 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1651 / CC1/2: 0.774 / Rpim(I) all: 0.249 / Rrim(I) all: 0.717 / % possible all: 92.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6EPB Resolution: 2.32→48.21 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.891 / SU B: 8.631 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.538 / ESU R Free: 0.274 / 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: 70.28 Å2 / Biso mean: 22.216 Å2 / Biso min: 9.9 Å2
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Refinement step | Cycle: final / Resolution: 2.32→48.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.32→2.38 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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