[English] 日本語
![](img/lk-miru.gif)
- PDB-7zy9: Structure of D165A/D167A double mutant of Chit33 from Trichoderma... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7zy9 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of D165A/D167A double mutant of Chit33 from Trichoderma harzianum complexed with chitintetraose. | ||||||
![]() | Endochitinase 33 | ||||||
![]() | HYDROLASE / Chitinase / endo-chitinase / glycoside hydrolase / fungal chitinase / Thichoderma harzianum / GH18 family / chitooligosaccharide / oligosaccharide / COS / chitin / chitosan / chitintetraose. | ||||||
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. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure-Function Insights into the Fungal Endo -Chitinase Chit33 Depict its Mechanism on Chitinous Material. Authors: Jimenez-Ortega, E. / Kidibule, P.E. / Fernandez-Lobato, M. / Sanz-Aparicio, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 82.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 58.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 859.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 861.9 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zyaC ![]() 2uy2S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 32511.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: 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 |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.41 % / Description: Prism bar shape |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 30% PEG 1500, 20% glycerol. Soaking conditions: 32% PEG 1500, 18% glycerol, 18 mM chitintetraose. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 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: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.78 Å / Num. obs: 44920 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.035 / Rrim(I) all: 0.09 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2190 / CC1/2: 0.883 / Rpim(I) all: 0.255 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2UY2 Resolution: 1.6→46.78 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.305 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 56.51 Å2 / Biso mean: 18.041 Å2 / Biso min: 8.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→46.78 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|