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- PDB-6kks: Structural insights into target DNA recognition by R2R3-type MYB ... -

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Basic information

Entry
Database: PDB / ID: 6kks
TitleStructural insights into target DNA recognition by R2R3-type MYB transcription factor
Components
  • DNA (5'-D(*AP*AP*AP*TP*TP*CP*TP*CP*CP*AP*AP*CP*CP*GP*CP*AP*TP*TP*TP*TP*C)-3')
  • DNA (5'-D(*CP*GP*AP*AP*AP*AP*TP*GP*CP*GP*GP*TP*TP*GP*GP*AP*GP*AP*AP*TP*T)-3')
  • Transcription factor WER
KeywordsDNA BINDING PROTEIN/DNA / Transcription factor / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


root hair cell differentiation / cell fate commitment / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor WER
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWang, B. / Luo, Q.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural insights into target DNA recognition by R2R3-MYB transcription factors.
Authors: Wang, B. / Luo, Q. / Li, Y. / Yin, L. / Zhou, N. / Li, X. / Gan, J. / Dong, A.
History
DepositionJul 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 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: Transcription factor WER
B: DNA (5'-D(*AP*AP*AP*TP*TP*CP*TP*CP*CP*AP*AP*CP*CP*GP*CP*AP*TP*TP*TP*TP*C)-3')
C: DNA (5'-D(*CP*GP*AP*AP*AP*AP*TP*GP*CP*GP*GP*TP*TP*GP*GP*AP*GP*AP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9594
Polymers26,9353
Non-polymers241
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-35 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.084, 63.927, 73.956
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcription factor WER / Myb-related protein 66 / AtMYB66 / Protein WEREWOLF


Mass: 14066.329 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WER / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9SEI0
#2: DNA chain DNA (5'-D(*AP*AP*AP*TP*TP*CP*TP*CP*CP*AP*AP*CP*CP*GP*CP*AP*TP*TP*TP*TP*C)-3')


Mass: 6317.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain DNA (5'-D(*CP*GP*AP*AP*AP*AP*TP*GP*CP*GP*GP*TP*TP*GP*GP*AP*GP*AP*AP*TP*T)-3')


Mass: 6551.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 48.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES pH 6.0, 30%(v/v) PEG600, 5%(w/v) PEG1000 and 10%(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.15→48.364 Å / Num. obs: 13918 / % possible obs: 99.6 % / Redundancy: 14.242 % / Biso Wilson estimate: 43.053 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.109 / Χ2: 1.064 / Net I/σ(I): 21.04 / Num. measured all: 198226
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.2814.3740.9353.531823221522140.9240.969100
2.28-2.4414.580.6175.5330342208120810.9740.64100
2.44-2.6314.5350.3768.728271194519450.9880.39100
2.63-2.8814.4960.25112.8226151180418040.9930.26100
2.88-3.2214.3230.12421.1823447163716370.9990.129100
3.22-3.7214.0360.06638.520492146014600.9990.068100
3.72-4.5413.7240.05348.916318124211890.9990.05595.7
4.54-6.413.960.05151.97139329989980.9990.053100
6.4-48.36412.6270.04355.374505955900.9990.04599.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H8A

1h8a


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.484 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 624 4.5 %RANDOM
Rwork0.2136 ---
obs0.215 13289 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.58 Å2 / Biso mean: 40.619 Å2 / Biso min: 21.43 Å2
Baniso -1Baniso -2Baniso -3
1--4.12 Å2-0 Å20 Å2
2--2.98 Å2-0 Å2
3---1.14 Å2
Refinement stepCycle: final / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms873 812 1 69 1755
Biso mean--30.67 38.79 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0151802
X-RAY DIFFRACTIONr_bond_other_d0.0020.021327
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.5252599
X-RAY DIFFRACTIONr_angle_other_deg1.19733072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6585105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.96522.38142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48515171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.85159
X-RAY DIFFRACTIONr_chiral_restr0.0610.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021461
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02414
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 36 -
Rwork0.275 984 -
all-1020 -
obs--99.9 %

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