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- PDB-6avv: Crystal structure of Arabidopsis thaliana SOBER1 -

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Basic information

Entry
Database: PDB / ID: 6avv
TitleCrystal structure of Arabidopsis thaliana SOBER1
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 / phospholipase A2 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 / molecular replacement / Resolution: 1.51003057388 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

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Assembly

Deposited unit
A: Carboxylesterase SOBER1


Theoretical massNumber of molelcules
Total (without water)25,0231
Polymers25,0231
Non-polymers00
Water3,621201
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)45.760, 52.290, 74.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 1.77 Å3/Da / Density % sol: 30.69 %
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 28, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.12_2829)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FJ2

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
RfactorNum. reflection% reflection
Rfree0.196198034887 1446 5.05241090147 %
Rwork0.168675261459 --
obs0.17001982761 28620 99.9580888516 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.8533055659 Å2
Refinement stepCycle: LAST / Resolution: 1.51003057388→34.4358696971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 0 201 1814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005016356544981679
X-RAY DIFFRACTIONf_angle_d0.8584903175062293
X-RAY DIFFRACTIONf_chiral_restr0.0638165296329256
X-RAY DIFFRACTIONf_plane_restr0.0068046113947294
X-RAY DIFFRACTIONf_dihedral_angle_d5.26374167441369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.5640.2155161467911420.201512482822660X-RAY DIFFRACTION99.9643239386
1.564-1.62660.2023713085951350.198883063212663X-RAY DIFFRACTION99.8928953945
1.6266-1.70060.2339305543651300.1901292249492709X-RAY DIFFRACTION99.8944405348
1.7006-1.79030.221728847261540.184845370642666X-RAY DIFFRACTION99.8937300744
1.7903-1.90250.2197659651791560.1849979898382676X-RAY DIFFRACTION100
1.9025-2.04930.2081572722641490.171885731352686X-RAY DIFFRACTION100
2.0493-2.25550.1909924446351370.1672918567912730X-RAY DIFFRACTION100
2.2555-2.58180.191733998631430.1716099594632731X-RAY DIFFRACTION99.9652173913
2.5818-3.25240.2006969835051660.1690155998672743X-RAY DIFFRACTION100
3.2524-34.44480.1723129403271340.1519295419822910X-RAY DIFFRACTION100

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