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- PDB-9fwy: Structure of the Nothoceros aenigmaticus LFY DNA-binding domain b... -

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Basic information

Entry
Database: PDB / ID: 9fwy
TitleStructure of the Nothoceros aenigmaticus LFY DNA-binding domain bound to DNA
Components
  • (DNA (29-MER)) x 2
  • Floricaula/leafy-like transcription factor
KeywordsDNA BINDING PROTEIN / transcription factor / DNA binding domain / gene regulation / hornwort
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
Floricaula/leafy protein / Floricaula/Leafy protein, SAM domain / Floricaula/leafy, DNA-binding C-terminal domain / Floricaula/leafy, C-terminal domain superfamily / Floricaula / Leafy protein SAM domain / DNA Binding Domain (C-terminal) Leafy/Floricaula
Similarity search - Domain/homology
DNA / DNA (> 10) / Floricaula/leafy-like transcription factor
Similarity search - Component
Biological speciesNothoceros aenigmaticus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsVerhage, L. / Zubieta, C. / Nanao, M.H. / Parcy, F.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: Structure of the Nothoceros aenigmaticus LFY DNA-binding domain bound to DNA
Authors: Verhage, L. / Zubieta, C. / Nanao, M.H. / Dumas, R.
History
DepositionJul 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Floricaula/leafy-like transcription factor
B: Floricaula/leafy-like transcription factor
F: DNA (29-MER)
G: DNA (29-MER)


Theoretical massNumber of molelcules
Total (without water)57,0064
Polymers57,0064
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-59 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.220, 90.900, 152.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Floricaula/leafy-like transcription factor


Mass: 19584.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nothoceros aenigmaticus (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: W8EDT4
#2: DNA chain DNA (29-MER)


Mass: 8980.765 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Nothoceros aenigmaticus (plant)
#3: DNA chain DNA (29-MER)


Mass: 8855.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Nothoceros aenigmaticus (plant)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 50 mM sodium acetate, pH 4.6, 8% PEG3350 / PH range: 4.4-5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.35→78 Å / Num. obs: 24681 / % possible obs: 95.2 % / Redundancy: 2.65 % / CC1/2: 0.996 / Rmerge(I) obs: 0.147 / Rrim(I) all: 0.181 / Net I/σ(I): 4.9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.35-2.412.09815980.2042.6171
2.41-2.472.38217310.1852.9451
2.47-2.541.76217920.3062.1691
2.54-2.621.58416820.4081.9521
2.62-2.711.13216640.611.3961
2.71-2.81.13215590.4651.4011
2.8-2.910.75315300.7260.9331
2.91-3.030.60414720.8290.741
3.03-3.160.39714360.9120.4881
3.16-3.320.24413680.9660.31
3.32-3.50.16512620.9830.2051
3.5-3.710.12812210.9860.1581
3.71-3.970.09811500.990.121
3.97-4.280.07410690.9940.091
4.28-4.690.0659510.9950.081
4.69-5.250.0599050.9960.0721
5.25-6.060.0627970.9950.0761
6.06-7.420.0526540.9970.0631
7.42-10.490.0415430.9970.051
10.49-780.0282970.9990.0351

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Processing

Software
NameVersionClassification
REFMACv5.8refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→78 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.297 613 4.8 %random
Rwork0.257 ---
obs0.259 12200 95 %-
Refinement stepCycle: LAST / Resolution: 2.9→78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2614 1183 0 16 3813

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