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- PDB-8s8q: Structure of the Interfilum paradoxum LFY DNA-binding domain boun... -

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Basic information

Entry
Database: PDB / ID: 8s8q
TitleStructure of the Interfilum paradoxum LFY DNA-binding domain bound to DNA
Components
  • DNA (5'-D(P*GP*GP*TP*GP*CP*AP*GP*CP*GP*AP*CP*CP*GP*GP*TP*AP*GP*CP*AP*AP*CP*GP*CP*A)-3')
  • DNA (5'-D(P*TP*GP*CP*GP*TP*TP*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*GP*CP*TP*GP*CP*AP*CP*T)-3')
  • Floricaula/leafy-like transcription factor
KeywordsDNA BINDING PROTEIN / transcription factor / protein-DNA complex / Interfilum paradoxum
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 speciesInterfilum paradoxum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsVerhage, L. / Zubieta, C. / Nanao, M.H.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: Structure of the Interfilum paradoxum LFY DNA-binding domain bound to DNA
Authors: Verhage, L. / Zubieta, C. / Nanao, M.H.
History
DepositionMar 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 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
D: DNA (5'-D(P*GP*GP*TP*GP*CP*AP*GP*CP*GP*AP*CP*CP*GP*GP*TP*AP*GP*CP*AP*AP*CP*GP*CP*A)-3')
B: Floricaula/leafy-like transcription factor
C: DNA (5'-D(P*TP*GP*CP*GP*TP*TP*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*GP*CP*TP*GP*CP*AP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)52,1764
Polymers52,1764
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, based on band shift assays, 2 LFY monomers bind co-operatively to DNA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.890, 144.890, 69.836
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Floricaula/leafy-like transcription factor


Mass: 18708.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Interfilum paradoxum LFY DNA-binding domain / Source: (gene. exp.) Interfilum paradoxum (plant) / Gene: KFL_007730030 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y1IRK2
#2: DNA chain DNA (5'-D(P*GP*GP*TP*GP*CP*AP*GP*CP*GP*AP*CP*CP*GP*GP*TP*AP*GP*CP*AP*AP*CP*GP*CP*A)-3')


Mass: 7429.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Interfilum paradoxum (plant)
#3: DNA chain DNA (5'-D(P*TP*GP*CP*GP*TP*TP*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*GP*CP*TP*GP*CP*AP*CP*T)-3')


Mass: 7328.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Interfilum paradoxum (plant)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 4.07 Å3/Da / Density % sol: 69.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 8000 30%, 10mM magnesium acetate / PH range: 5-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8734 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8734 Å / Relative weight: 1
ReflectionResolution: 2.72→47.43 Å / Num. obs: 22512 / % possible obs: 99.5 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.159 / Net I/σ(I): 9.26
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.72-2.793.37515880.0953.7761
2.79-2.872.58516020.2072.8471
2.87-2.952.20815740.2242.41
2.95-3.041.62615250.4711.7531
3.04-3.141.15815030.6551.2421
3.14-3.250.83114050.7820.891
3.25-3.380.56413850.8760.6051
3.38-3.510.39413480.9490.4231
3.51-3.670.29312780.9680.3141
3.67-3.850.212190.990.2141
3.85-4.060.14711620.9930.1571
4.06-4.30.12411040.9950.1331
4.3-4.60.11610510.9950.1241
4.6-4.970.0989700.9960.1051
4.97-5.440.0879010.9980.0931
5.44-6.090.088090.9970.0861
6.09-7.030.087220.9970.0861
7.03-8.610.0476130.9990.0511
8.61-12.170.0294790.9990.0311
12.17-47.30.02527410.0271

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→47.43 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 21.933 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R: 0.705 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23693 891 5 %RANDOM
Rwork0.19376 ---
obs0.19587 16920 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.715 Å2
Baniso -1Baniso -2Baniso -3
1--3.54 Å2-1.77 Å2-0 Å2
2---3.54 Å20 Å2
3---11.5 Å2
Refinement stepCycle: 1 / Resolution: 2.95→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2599 985 0 31 3615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123756
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163080
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.8495259
X-RAY DIFFRACTIONr_angle_other_deg0.5381.7517141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.44522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69710502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023753
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02808
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.9797.9071286
X-RAY DIFFRACTIONr_mcbond_other5.9637.9091286
X-RAY DIFFRACTIONr_mcangle_it8.88214.2041604
X-RAY DIFFRACTIONr_mcangle_other8.88714.211605
X-RAY DIFFRACTIONr_scbond_it7.7829.1522470
X-RAY DIFFRACTIONr_scbond_other7.7819.1562471
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.18416.5183656
X-RAY DIFFRACTIONr_long_range_B_refined17.9499.494646
X-RAY DIFFRACTIONr_long_range_B_other17.94299.54647
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.492 65 -
Rwork0.477 1246 -
obs--99.92 %

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