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- PDB-6ry3: Structure of the WUS homeodomain -

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Basic information

Entry
Database: PDB / ID: 6ry3
TitleStructure of the WUS homeodomain
ComponentsProtein WUSCHEL
KeywordsDNA BINDING PROTEIN / Homeodomain Transcription factor
Function / homology
Function and homology information


stomium development / anther development / axillary shoot meristem initiation / stem cell population maintenance / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleus
Similarity search - Function
Protein WUSCHEL-like / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
ACETYL GROUP / Protein WUSCHEL
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.374 Å
AuthorsSloan, J.J. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL.
Authors: Sloan, J. / Hakenjos, J.P. / Gebert, M. / Ermakova, O. / Gumiero, A. / Stier, G. / Wild, K. / Sinning, I. / Lohmann, J.U.
History
DepositionJun 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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: Protein WUSCHEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1775
Polymers8,9491
Non-polymers2284
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-12 kcal/mol
Surface area5110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.120, 43.120, 82.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Protein WUSCHEL / AtWUS / Plant growth activator 6


Mass: 8949.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WUS, PGA6, At2g17950, T27K22.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SB92
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2.5 M ammonium sulfate 0.05 M MES (pH 6.0) 0.01 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.374→38.17 Å / Num. obs: 16816 / % possible obs: 99.85 % / Redundancy: 24.5 % / Biso Wilson estimate: 13.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03774 / Rpim(I) all: 0.00818 / Net I/σ(I): 61.11
Reflection shellResolution: 1.374→1.423 Å / Num. unique obs: 1628 / Rpim(I) all: 0.03016

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HDD

3hdd


Resolution: 1.374→38.166 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 22.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 836 4.97 %
Rwork0.1844 15971 -
obs0.1859 16807 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.51 Å2 / Biso mean: 19.5167 Å2 / Biso min: 6.64 Å2
Refinement stepCycle: final / Resolution: 1.374→38.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms560 0 14 50 624
Biso mean--50.2 28.4 -
Num. residues----65
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01602
X-RAY DIFFRACTIONf_angle_d1.047804
X-RAY DIFFRACTIONf_chiral_restr0.0879
X-RAY DIFFRACTIONf_plane_restr0.006102
X-RAY DIFFRACTIONf_dihedral_angle_d16.095376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3736-1.45960.31221450.25322573271899
1.4596-1.57230.24941470.21425982745100
1.5723-1.73060.20871250.202326302755100
1.7306-1.9810.20351330.169126472780100
1.981-2.49580.19151480.15826702818100
2.4958-38.18070.20881380.185528532991100

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