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- PDB-2vy1: Structure of LEAFY transcription factor from Arabidopsis thaliana... -

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Basic information

Entry
Database: PDB / ID: 2vy1
TitleStructure of LEAFY transcription factor from Arabidopsis thaliana in complex with DNA from AP1 promoter
Components
  • 5'-D(*TP*TP*AP*CP*GP*GP*AP*CP*CP*AP *CP*TP*GP*GP*TP*CP*CP*TP*TP*CP)-3'
  • PROTEIN LEAFY
KeywordsTRANSCRIPTION / DNA-BINDING / POLYMORPHISM / DEVELOPMENTAL PROTEIN / TRANSCRIPTION REGULATION / HOMEOTIC GENES / FLOWERING / NUCLEUS / DIFFERENTIATION / FLOWER DEVELOPMENT / ACTIVATOR / COILED COIL
Function / homology
Function and homology information


floral meristem determinacy / maintenance of inflorescence meristem identity / gibberellic acid mediated signaling pathway / flower development / chromatin DNA binding / sequence-specific DNA binding / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity / protein homodimerization activity / nucleus
Similarity search - Function
Protein LEAFY / Protein LEAFY / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein LEAFY
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.104 Å
AuthorsHames, C. / Ptchelkine, D. / Grimm, C. / Thevenon, E. / Moyroud, E. / Gerard, F. / Martiel, J.L. / Benlloch, R. / Parcy, F. / Muller, C.W.
CitationJournal: Embo J. / Year: 2008
Title: Structural Basis for Leafy Floral Switch Function and Similarity with Helix-Turn-Helix Proteins.
Authors: Hames, C. / Ptchelkine, D. / Grimm, C. / Thevenon, E. / Moyroud, E. / Gerard, F. / Martiel, J.L. / Benlloch, R. / Parcy, F. / Muller, C.W.
History
DepositionJul 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN LEAFY
W: 5'-D(*TP*TP*AP*CP*GP*GP*AP*CP*CP*AP *CP*TP*GP*GP*TP*CP*CP*TP*TP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)28,1002
Polymers28,1002
Non-polymers00
Water1,22568
1
A: PROTEIN LEAFY
W: 5'-D(*TP*TP*AP*CP*GP*GP*AP*CP*CP*AP *CP*TP*GP*GP*TP*CP*CP*TP*TP*CP)-3'

A: PROTEIN LEAFY
W: 5'-D(*TP*TP*AP*CP*GP*GP*AP*CP*CP*AP *CP*TP*GP*GP*TP*CP*CP*TP*TP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)56,2004
Polymers56,2004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6080 Å2
ΔGint-29 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.390, 98.390, 176.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein PROTEIN LEAFY / LEAFY


Mass: 21892.002 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN, RESIDUES 231-424
Source method: isolated from a genetically manipulated source
Details: NONE / Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Tissue: FLOWER MERISTEM / Organ: FLOWER / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTABLUE PLYS / References: UniProt: Q00958
#2: DNA chain 5'-D(*TP*TP*AP*CP*GP*GP*AP*CP*CP*AP *CP*TP*GP*GP*TP*CP*CP*TP*TP*CP)-3' / DNA AP1 SITE


Mass: 6208.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ARABIDOPSIS THALIANA (thale cress)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN W HAS MICROHETEROGENEITY AT POSITIONS 1(DT/DA), 2(DG/DT), 4(DA/DC), 11(DG/DC), 18(DG/DT) AND 20(DA/DC).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 5.14 Å3/Da / Density % sol: 78.63 % / Description: NONE
Crystal growpH: 7
Details: 10% PEG 400, 100 MM KCL, 10 MM CACL2, 50 MM HEPES (NAOH) PH 7.0

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2007
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 29859 / % possible obs: 97.4 % / Observed criterion σ(I): 3 / Redundancy: 16.9 % / Biso Wilson estimate: 41.43 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 38.5
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 12 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 5 / % possible all: 83.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.104→19.429 Å / SU ML: 0.27 / σ(F): 1.38 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2515 1521 5.09 %
Rwork0.2245 --
obs0.2259 29857 99.52 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.693 Å2 / ksol: 0.451 e/Å3
Displacement parametersBiso mean: 44.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.5315 Å20 Å20 Å2
2--1.5315 Å20 Å2
3----3.0631 Å2
Refinement stepCycle: LAST / Resolution: 2.104→19.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 527 0 68 1921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051983
X-RAY DIFFRACTIONf_angle_d1.0262803
X-RAY DIFFRACTIONf_dihedral_angle_d22.301778
X-RAY DIFFRACTIONf_chiral_restr0.055295
X-RAY DIFFRACTIONf_plane_restr0.003273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1037-2.17160.27221220.25192493X-RAY DIFFRACTION98
2.1716-2.24910.26211370.25282535X-RAY DIFFRACTION100
2.2491-2.3390.26451440.23972528X-RAY DIFFRACTION100
2.339-2.44520.26681430.23032528X-RAY DIFFRACTION100
2.4452-2.57390.25641440.24032533X-RAY DIFFRACTION100
2.5739-2.73470.26331390.2322579X-RAY DIFFRACTION100
2.7347-2.94520.2541370.23342551X-RAY DIFFRACTION100
2.9452-3.24040.28341250.2312598X-RAY DIFFRACTION100
3.2404-3.70640.22481560.20782606X-RAY DIFFRACTION100
3.7064-4.65910.23421380.18492656X-RAY DIFFRACTION100
4.6591-19.430.24151360.21892729X-RAY DIFFRACTION97

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