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- PDB-6rsn: SOSEKI polymerising domain (SOK4 D85A mutant) -

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Basic information

Entry
Database: PDB / ID: 6rsn
TitleSOSEKI polymerising domain (SOK4 D85A mutant)
ComponentsUPSTREAM OF FLC-like protein (DUF966)
KeywordsSIGNALING PROTEIN / polymeriser / plant protein / ubiquitin-like fold / polarity protein
Function / homologyProtein SOSEKI / Protein SOSEKI, magnoliopsida / SOSEKI protein DIX-like domain / plasma membrane / UPSTREAM OF FLC-like protein (DUF966) / At3g46110
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsFiedler, M. / Bienz, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105192713 United Kingdom
CitationJournal: Cell / Year: 2020
Title: DIX Domain Polymerization Drives Assembly of Plant Cell Polarity Complexes.
Authors: van Dop, M. / Fiedler, M. / Mutte, S. / de Keijzer, J. / Olijslager, L. / Albrecht, C. / Liao, C.Y. / Janson, M.E. / Bienz, M. / Weijers, D.
History
DepositionMay 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPSTREAM OF FLC-like protein (DUF966)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2352
Polymers11,1381
Non-polymers961
Water68538
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, the wild type domain forms concentration dependent polymers, which can be observed in the crystal even in the polymerisation mutant (D85A)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-10 kcal/mol
Surface area5780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.659, 47.659, 67.971
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein UPSTREAM OF FLC-like protein (DUF966)


Mass: 11138.453 Da / Num. of mol.: 1 / Mutation: D85A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g46110 / Plasmid: pLipK
Details (production host): pET based vector expressing 6xHis and Lipoyl-tag separated by TEV cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRARE2 / References: UniProt: F4J7X6, UniProt: Q8GY65*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2 Å3/Da / Density % sol: 38.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.69 M ammonium sulfate, 200 mM NaCl, 100 mM HEPES pH 7.0
Temp details: controlled environment at 18C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→35.28 Å / Num. obs: 9612 / % possible obs: 99.45 % / Redundancy: 20 % / Biso Wilson estimate: 25.45 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.07499 / Rpim(I) all: 0.01717 / Rrim(I) all: 0.07696 / Net I/σ(I): 33.91
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 20.2 % / Rmerge(I) obs: 0.6597 / Mean I/σ(I) obs: 5.81 / Num. unique obs: 949 / CC1/2: 0.935 / CC star: 0.983 / Rpim(I) all: 0.1492 / Rrim(I) all: 0.6766 / % possible all: 99.06

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Processing

Software
NameVersionClassification
REFMAC5.8.0256refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD
Starting model: model

Resolution: 1.7→35.28 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.242 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.111
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 512 5.3 %RANDOM
Rwork0.1846 ---
obs0.1861 9612 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.94 Å2 / Biso mean: 28.28 Å2 / Biso min: 17.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.17 Å20 Å2
2--0.33 Å2-0 Å2
3----1.08 Å2
Refinement stepCycle: final / Resolution: 1.7→35.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 0 5 38 802
Biso mean--73.45 38.06 -
Num. residues----92
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.012792
X-RAY DIFFRACTIONr_angle_refined_deg2.1771.6271077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.977593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95421.08746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.715124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.822156
X-RAY DIFFRACTIONr_chiral_restr0.1440.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02628
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 46 -
Rwork0.186 639 -
all-685 -
obs--98.7 %
Refinement TLS params.Method: refined / Origin x: 17.6192 Å / Origin y: 21.9283 Å / Origin z: 18.4449 Å
111213212223313233
T0.0405 Å2-0.0331 Å2-0.0068 Å2-0.0646 Å20.0562 Å2--0.0875 Å2
L1.9914 °2-0.2289 °21.3452 °2-1.2319 °2-0.5001 °2--3.0921 °2
S0.235 Å °-0.2742 Å °-0.2341 Å °0.088 Å °0.0347 Å °0.2071 Å °0.1402 Å °-0.3231 Å °-0.2697 Å °

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