+Open data
-Basic information
Entry | Database: PDB / ID: 6avx | ||||||
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Title | Crystal structure of Arabidopsis thaliana SOBER1 F65L | ||||||
Components | Carboxylesterase SOBER1 | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase / plant deacetylase / hypersensitive response | ||||||
Function / homology | Function and homology information short-chain carboxylesterase activity / regulation of plant-type hypersensitive response / palmitoyl-(protein) hydrolase activity / phosphatidic acid biosynthetic process / defense response to other organism / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / phospholipase A2 activity / carboxylic ester hydrolase activity / fatty acid metabolic process / defense response to bacterium / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.271 Å | ||||||
Authors | Burger, M. / Willige, B.C. / Chory, J. | ||||||
Citation | Journal: Nat Commun / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6avx.cif.gz | 97 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6avx.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 6avx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/6avx ftp://data.pdbj.org/pub/pdb/validation_reports/av/6avx | HTTPS FTP |
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-Related structure data
Related structure data | 6avvSC 6avwC 6avyC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Monomer as determined by gel filtration |
-Components
#1: Protein | Mass: 24988.555 Da / Num. of mol.: 1 / Mutation: F65L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOBER1, At4g22305 / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q84WK4, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.69 % |
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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: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2016 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→39.032 Å / Num. obs: 47288 / % possible obs: 98 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.02519 / Net I/σ(I): 18.77 |
Reflection shell | Resolution: 1.27→1.32 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.05704 / Mean I/σ(I) obs: 9.09 / Num. unique obs: 4531 / CC1/2: 0.987 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AVV Resolution: 1.271→39.032 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.21 Å2 / Biso mean: 14.777 Å2 / Biso min: 4.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.271→39.032 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
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