+Open data
-Basic information
Entry | Database: PDB / ID: 6avv | ||||||
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Title | Crystal structure of Arabidopsis thaliana SOBER1 | ||||||
Components | Carboxylesterase SOBER1 | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase / plant deacetylase / hypersensitive response | ||||||
Function / homology | Function and homology information regulation of plant-type hypersensitive response / short-chain carboxylesterase activity / palmitoyl-(protein) hydrolase activity / phosphatidic acid biosynthetic process / defense response to other organism / phospholipase A2 activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / 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 / molecular replacement / Resolution: 1.51003057388 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 | 6avv.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6avv.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 6avv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6avv_validation.pdf.gz | 427.7 KB | Display | wwPDB validaton report |
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Full document | 6avv_full_validation.pdf.gz | 429.8 KB | Display | |
Data in XML | 6avv_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 6avv_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/6avv ftp://data.pdbj.org/pub/pdb/validation_reports/av/6avv | HTTPS FTP |
-Related structure data
Related structure data | 6avwC 6avxC 6avyC 1fj2S 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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-Components
#1: Protein | Mass: 25022.570 Da / Num. of mol.: 1 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: 1.77 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: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
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: 1 Å / Relative weight: 1 |
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: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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