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Open data
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Basic information
Entry | Database: PDB / ID: 7zya | ||||||
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Title | Structure of Chit33 from Trichoderma harzianum. | ||||||
![]() | Endochitinase 33 | ||||||
![]() | HYDROLASE / Chitinase / endo-chitinase / glycoside hydrolase / fungal chitinase / Thichoderma harzianum / GH18 family / chitooligosaccharide / oligosaccharide / COS / chitin / chitosan / chitintetraose. / HYDROLASE. | ||||||
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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.7 KB | Display | ![]() |
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PDB format | ![]() | 59.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7zy9C ![]() 2uy2S C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 32613.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Chemical | ChemComp-TRS / | ||||
#3: Chemical | ChemComp-PEG / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.93 % / Description: Diamond shape |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 20% PEG 1500, 20% Glycerol. Soaking conditions: 23% PEG 1500, 20% Glycerol, 2mM Triacetyl-chitotriose. Cryoprotectant conditions: 30% PEG 1500, 20% glycerol. |
-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: Feb 17, 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: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→46.89 Å / Num. obs: 127452 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.12→1.14 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6255 / CC1/2: 0.844 / Rpim(I) all: 0.305 / Rrim(I) all: 0.763 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2UY2 Resolution: 1.12→46.89 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.407 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.028 / 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: 57.74 Å2 / Biso mean: 16.648 Å2 / Biso min: 9.91 Å2
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Refinement step | Cycle: final / Resolution: 1.12→46.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.12→1.149 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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