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- PDB-4ude: An oligomerization domain confers pioneer properties to the LEAFY... -

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Basic information

Entry
Database: PDB / ID: 4ude
TitleAn oligomerization domain confers pioneer properties to the LEAFY master floral regulator
ComponentsGINLFY PROTEIN
KeywordsTRANSCRIPTION / SAM / OLIGOMERISATION
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
Floricaula/leafy-like transcription factor
Similarity search - Component
Biological speciesGINKGO BILOBA (maidenhair tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsNanao, M.H. / Sayou, C. / Dumas, R. / Parcy, F.
CitationJournal: Nat.Commun. / Year: 2016
Title: A Sam Oligomerization Domain Shapes the Genomic Binding Landscape of the Leafy Transcription Factor
Authors: Sayou, C. / Nanao, M.H. / Jamin, M. / Pose, D. / Thevenon, E. / Gregoire, L. / Tichtinsky, G. / Denay, G. / Ott, F. / Peirats Llobet, M. / Schmid, M. / Dumas, R. / Parcy, F.
History
DepositionDec 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references / Structure summary
Revision 1.2May 4, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GINLFY PROTEIN
B: GINLFY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9045
Polymers25,5252
Non-polymers3783
Water1,838102
1
A: GINLFY PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,7631
Polymers12,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GINLFY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1414
Polymers12,7631
Non-polymers3783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.095, 81.095, 78.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8653, -0.5012, -0.0068), (0.5012, 0.865, -0.0124), (0.0122, 0.0073, 0.999)
Vector: 0.05466, 0.1245, -6.94)

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Components

#1: Protein GINLFY PROTEIN / LEAFY


Mass: 12762.703 Da / Num. of mol.: 2 / Fragment: RESIDUES 54-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GINKGO BILOBA (maidenhair tree) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LLY6
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGENBANK AF108228.1

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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: 2.92 Å3/Da / Density % sol: 57.86 % / Description: NONE
Crystal growDetails: 25 MM TRIS-HCL PH 8.8, 40 MM AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: May 11, 2011 / Details: KB MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 14004 / % possible obs: 99.3 % / Observed criterion σ(I): -1 / Redundancy: 4.1 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.67
Reflection shellResolution: 2.24→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.89 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.25→52.34 Å / Cor.coef. Fo:Fc: 0.9456 / Cor.coef. Fo:Fc free: 0.9257 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 709 5.09 %RANDOM
Rwork0.1877 ---
obs0.1896 13917 --
Displacement parametersBiso mean: 46.76 Å2
Baniso -1Baniso -2Baniso -3
1--3.0645 Å20 Å20 Å2
2---3.0645 Å20 Å2
3---6.129 Å2
Refine analyzeLuzzati coordinate error obs: 0.262 Å
Refinement stepCycle: LAST / Resolution: 2.25→52.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 25 102 1462
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011369HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.031827HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d532SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes191HARMONIC5
X-RAY DIFFRACTIONt_it1369HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion17.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion172SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1609SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.43 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2823 153 5.33 %
Rwork0.2268 2718 -
all0.2298 2871 -

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