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Open data
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Basic information
Entry | Database: PDB / ID: 7eox | ||||||
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Title | Protease structure from Euphorbia resinifera | ||||||
![]() | Protease | ||||||
![]() | PLANT PROTEIN / Euphorbia resinifera / plant latex / serine protease | ||||||
Function / homology | IODIDE ION![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Siritapetawee, J. / Attarataya, J. / Charoenwattanasatien, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Sequence analysis and crystal structure of a glycosylated protease from Euphorbia resinifera latex for its proteolytic activity aspect. Authors: Siritapetawee, J. / Attarataya, J. / Charoenwattanasatien, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 259.1 KB | Display | ![]() |
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PDB format | ![]() | 208.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 864.2 KB | Display | ![]() |
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Full document | ![]() | 871.1 KB | Display | |
Data in XML | ![]() | 50.3 KB | Display | |
Data in CIF | ![]() | 74 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 69006.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Polysaccharide | beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Sugar | #4: Chemical | ChemComp-IOD / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M sodium idodide (0.2 M), 0.1M Bis-Tris propane pH 8.5, 20% W/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2018 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.7→64.16 Å / Num. obs: 168106 / % possible obs: 99 % / Redundancy: 5.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.08 / Rrim(I) all: 0.141 / Net I/σ(I): 9.7 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 26.667 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→60.01 Å
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Refine LS restraints |
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