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- PDB-2vy2: Structure of LEAFY transcription factor from Arabidopsis thaliana... -

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Basic information

Entry
Database: PDB / ID: 2vy2
TitleStructure of LEAFY transcription factor from Arabidopsis thaliana in complex with DNA from AG-I promoter
Components
  • 5'-D(*AP*TP*TP*TP*AP*AP*TP*CP*CP*AP *AP*TP*GP*GP*TP*TP*AP*CP*AP*A)-3'
  • PROTEIN LEAFY
KeywordsTRANSCRIPTION / DNA-BINDING / POLYMORPHISM / DEVELOPMENTAL PROTEIN TRANSCRIPTION REGULATION / HOMEOTIC GENES / ACTIVATOR / DIFFERENTIATION FLOWER DEVELOPMENT / FLOWERING / COILED COIL GENES
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 ...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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.1Jan 18, 2012Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,0082
Polymers28,0082
Non-polymers00
Water82946
1
A: PROTEIN LEAFY
W: 5'-D(*AP*TP*TP*TP*AP*AP*TP*CP*CP*AP *AP*TP*GP*GP*TP*TP*AP*CP*AP*A)-3'

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


Theoretical massNumber of molelcules
Total (without water)56,0164
Polymers56,0164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6140 Å2
ΔGint-31 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.850, 98.850, 177.400
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
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Tissue: FLOWER MERISTEM / Description: NONE / Organ: FLOWER / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTABLUE(DE3)PLYS / References: UniProt: Q00958
#2: DNA chain 5'-D(*AP*TP*TP*TP*AP*AP*TP*CP*CP*AP *AP*TP*GP*GP*TP*TP*AP*CP*AP*A)-3' / DNA AG-I SITE


Mass: 6116.004 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.: 46 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN W HAS MICROHETEROGENEITY AT POSITIONS 1(DA/DT), 4(DT/DG), 5(DA/DT), 7(DT/DA), 11(DA/DT), ...CHAIN W HAS MICROHETEROGENEITY AT POSITIONS 1(DA/DT), 4(DT/DG), 5(DA/DT), 7(DT/DA), 11(DA/DT), 15(DT/DA) 17(DA/DT), AND 18(DC/DA).

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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: 5.21 Å3/Da / Density % sol: 78.94 % / 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: ID29 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 328932 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 14 % / Biso Wilson estimate: 38.53 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VY1

2vy1


Resolution: 2.3→19.951 Å / SU ML: 0.33 / σ(F): 2.05 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2619 1183 5.05 %
Rwork0.23 --
obs0.2315 23413 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.94 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 46.22 Å2
Baniso -1Baniso -2Baniso -3
1--1.6689 Å20 Å20 Å2
2---1.6689 Å20 Å2
3----6.537 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 565 0 46 1937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012004
X-RAY DIFFRACTIONf_angle_d1.3942838
X-RAY DIFFRACTIONf_dihedral_angle_d21.327785
X-RAY DIFFRACTIONf_chiral_restr0.071298
X-RAY DIFFRACTIONf_plane_restr0.005269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40450.31631450.28762701X-RAY DIFFRACTION100
2.4045-2.53110.27561490.26882726X-RAY DIFFRACTION100
2.5311-2.68930.27681440.25062728X-RAY DIFFRACTION100
2.6893-2.89640.29721560.25472736X-RAY DIFFRACTION100
2.8964-3.18680.27511340.26362773X-RAY DIFFRACTION100
3.1868-3.64550.27481550.22672768X-RAY DIFFRACTION100
3.6455-4.58370.22381580.18542819X-RAY DIFFRACTION100
4.5837-19.95220.23531420.19182979X-RAY DIFFRACTION99

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