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- PDB-8hw8: Crystal structure of Heterodera glycines chitinase 2 D129A/E131A ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hw8 | ||||||||||||
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Title | Crystal structure of Heterodera glycines chitinase 2 D129A/E131A mutant in complex with nodulation factor SmNF-V (C16:2, S) | ||||||||||||
![]() | Chitinase![]() | ||||||||||||
![]() | ![]() ![]() | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Chen, W. / Chen, Q. / Wang, D. / Yang, Q. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Heterodera glycines chitinase 2 D129A/E131A mutant in complex with nodulation factor SmNF-V (C16:2, S) Authors: Chen, W. / Chen, Q. / Wang, D. / Yang, Q. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.3 KB | Display | ![]() |
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PDB format | ![]() | 63.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 39279.551 Da / Num. of mol.: 1 / Mutation: D129A,E131A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() ![]() |
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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-(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-6-O-sulfo-beta-D-glucopyranose Type: oligosaccharide ![]() 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![]() |
-Non-polymers , 3 types, 289 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-68X / ( Mass: 413.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H39NO6 / Feature type: SUBJECT OF INVESTIGATION |
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#5: Chemical | ChemComp-PEG / ![]() |
#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: 2.04 Å3/Da / Density % sol: 39.58 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 M ammonium acetate, 0.1 M Bis-tris, pH 5.5, and 20% PEG 10,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.57→29.65 Å / Num. obs: 43220 / % possible obs: 98 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.47 Å2 / Rmerge(I) obs: 0.06299 / Rsym value: 0.06815 / Net I/σ(I): 15.09 |
Reflection shell | Resolution: 1.57→1.63 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.5986 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 4267 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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: 1.57→29.65 Å
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Refine LS restraints |
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LS refinement shell |
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