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- PDB-6avx: Crystal structure of Arabidopsis thaliana SOBER1 F65L -

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Basic information

Entry
Database: PDB / ID: 6avx
TitleCrystal structure of Arabidopsis thaliana SOBER1 F65L
ComponentsCarboxylesterase SOBER1
KeywordsHYDROLASE / alpha/beta hydrolase / plant deacetylase / hypersensitive response
Function / homology
Function and homology information


short-chain carboxylesterase activity / regulation of plant-type hypersensitive response / phosphatidic acid biosynthetic process / defense response to other organism / A2-type glycerophospholipase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity / fatty acid metabolic process / defense response to bacterium
Similarity search - Function
: / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Carboxylesterase SOBER1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.271 Å
AuthorsBurger, M. / Willige, B.C. / Chory, J.
CitationJournal: 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
DepositionSep 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxylesterase SOBER1


Theoretical massNumber of molelcules
Total (without water)24,9891
Polymers24,9891
Non-polymers00
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.500, 52.080, 75.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsMonomer as determined by gel filtration

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Components

#1: Protein Carboxylesterase SOBER1 / Phospholipase A2 SOBER1 / Protein SUPPRESSOR OF AVRBST-ELICITED RESISTANCE 1


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 16% (v/v) PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AVV

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
RfactorNum. reflection% reflection
Rfree0.1657 2343 4.95 %
Rwork0.1501 --
obs0.1509 47287 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.21 Å2 / Biso mean: 14.777 Å2 / Biso min: 4.64 Å2
Refinement stepCycle: final / Resolution: 1.271→39.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 0 311 1905
Biso mean---27.76 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071671
X-RAY DIFFRACTIONf_angle_d0.9492285
X-RAY DIFFRACTIONf_chiral_restr0.078256
X-RAY DIFFRACTIONf_plane_restr0.008293
X-RAY DIFFRACTIONf_dihedral_angle_d19.959610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.271-1.2970.18081310.16132507263894
1.297-1.32520.18921230.16072596271998
1.3252-1.3560.16361430.16372621276499
1.356-1.38990.18191420.15652617275999
1.3899-1.42750.1611390.1512644278399
1.4275-1.46950.16061240.15432685280999
1.4695-1.51690.16911520.1526382790100
1.5169-1.57120.18381480.141126532801100
1.5712-1.63410.15591360.149426782814100
1.6341-1.70840.14861480.145226482796100
1.7084-1.79850.14911310.148627052836100
1.7985-1.91120.14561580.145326682826100
1.9112-2.05870.16551250.137127302855100
2.0587-2.26590.14361120.138627232835100
2.2659-2.59370.15031400.14552710285099
2.5937-3.26760.16971430.14572751289499
3.2676-39.05010.1941480.17162370251883

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