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Open data
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Basic information
Entry | Database: PDB / ID: 6avv | ||||||
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Title | Crystal structure of Arabidopsis thaliana SOBER1 | ||||||
![]() | Carboxylesterase SOBER1 | ||||||
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Function / homology | ![]() short-chain carboxylesterase activity / regulation of plant-type hypersensitive response / palmitoyl-(protein) hydrolase activity / phosphatidic acid biosynthetic process / defense response to other organism / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Burger, M. / Willige, B.C. / Chory, J. | ||||||
![]() | ![]() Title: A hydrophobic anchor mechanism defines a deacetylase family that suppresses host response against YopJ effectors. Authors: Burger, M. / Willige, B.C. / Chory, 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 | ![]() | 71.5 KB | Display | ![]() |
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PDB format | ![]() | 41.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6avwC ![]() 6avxC ![]() 6avyC ![]() 1fj2S 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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Unit cell |
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Components
#1: Protein | Mass: 25022.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q84WK4, ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.69 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 16% (v/v) PEG 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2015 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.51→34.44 Å / Num. obs: 28632 / % possible obs: 99.94 % / Redundancy: 13.5 % / Biso Wilson estimate: 15.2127543409 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08223 / Rpim(I) all: 0.02324 / Net I/σ(I): 21.74 |
Reflection shell | Resolution: 1.51→1.564 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 4.58 / Num. unique obs: 2802 / CC1/2: 0.922 / Rpim(I) all: 0.2317 / % possible all: 99.96 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1FJ2 Resolution: 1.51003057388→34.4358696971 Å / SU ML: 0.141431086976 / Cross valid method: FREE R-VALUE / σ(F): 1.34349226796 / Phase error: 19.3162499903
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.8533055659 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51003057388→34.4358696971 Å
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Refine LS restraints |
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LS refinement shell |
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