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Open data
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Basic information
Entry | Database: PDB / ID: 6awv | ||||||
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Title | Ara h 8.01 in complex with epicatechin | ||||||
![]() | Ara h 8 allergen | ||||||
![]() | PROTEIN BINDING / PLANT PROTEIN / PEANUT / ALLERGEN | ||||||
Function / homology | ![]() response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Offermann, L.R. / Perdue, M. / McBride, J. / Hurlburt, B.K. / Maleki, S.J. / Pote, S.S. / Chruszcz, M. | ||||||
![]() | ![]() Title: Structure of PR-10 Allergen Ara h 8.01. Authors: Offermann, L.R. / Yarbrough, J. / McBride, J. / Hurlburt, B.K. / Maleki, S.J. / Pote, S.S. / Chruszcz, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.7 KB | Display | ![]() |
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PDB format | ![]() | 154 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6awrC ![]() 6awsC ![]() 6awtC ![]() 6awuC ![]() 6awwC ![]() 6awxC ![]() 6awyC ![]() 6awzC ![]() 6ax0C ![]() 4mapS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 16842.014 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-28E / ( #3: Chemical | ChemComp-BEZ / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200 mM magnesium chloride hexahydrate, 100 mM HEPES, pH 7.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2013 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→40 Å / Num. obs: 16860 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.035 / Rrim(I) all: 0.071 / Rsym value: 0.046 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 817 / Rpim(I) all: 0.324 / Rrim(I) all: 0.633 / Rsym value: 0.45 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MAP Resolution: 2.55→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / ESU R: 0.855 / ESU R Free: 0.324 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.461 Å2
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Refinement step | Cycle: 1 / Resolution: 2.55→40 Å
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Refine LS restraints |
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