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- PDB-6j9c: Crystal structure of Arabidopsis thaliana transcription factor LE... -

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Basic information

Entry
Database: PDB / ID: 6j9c
TitleCrystal structure of Arabidopsis thaliana transcription factor LEC2-DNA complex
Components
  • B3 domain-containing transcription factor LEC2
  • DNA (5'-D(*CP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3')
  • DNA (5'-D(*GP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3')
KeywordsTRANSCRIPTION/DNA / flowering time regulation / B3 domain / DNA-binding / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


positive regulation of auxin biosynthetic process / somatic embryogenesis / seed oilbody biogenesis / seed maturation / embryo development ending in seed dormancy / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
B3 domain-containing transcription factor LEC2-like / DNA-binding pseudobarrel domain / At1g16640 B3 domain / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / B3 domain-containing transcription factor LEC2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.102 Å
AuthorsHu, H. / Du, J.
CitationJournal: Nat.Plants / Year: 2019
Title: Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis.
Authors: Tao, Z. / Hu, H. / Luo, X. / Jia, B. / Du, J. / He, Y.
History
DepositionJan 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B3 domain-containing transcription factor LEC2
B: DNA (5'-D(*GP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3')
C: DNA (5'-D(*CP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3')
D: B3 domain-containing transcription factor LEC2
E: DNA (5'-D(*GP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3')
F: DNA (5'-D(*CP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)46,9666
Polymers46,9666
Non-polymers00
Water00
1
A: B3 domain-containing transcription factor LEC2
B: DNA (5'-D(*GP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3')
C: DNA (5'-D(*CP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)23,4833
Polymers23,4833
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-24 kcal/mol
Surface area10710 Å2
MethodPISA
2
D: B3 domain-containing transcription factor LEC2
E: DNA (5'-D(*GP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3')
F: DNA (5'-D(*CP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)23,4833
Polymers23,4833
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-22 kcal/mol
Surface area10940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.073, 96.601, 99.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein B3 domain-containing transcription factor LEC2 / Protein LEAFY COTYLEDON 2


Mass: 14306.181 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LEC2, At1g28300, F3H9.5 / Plasmid: PET22b / Production host: Escherichia coli BL21 (DE3) (bacteria) / Strain (production host): BL21 (DE3) / Variant (production host): RIL / References: UniProt: Q1PFR7
#2: DNA chain DNA (5'-D(*GP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3')


Mass: 4615.006 Da / Num. of mol.: 2 / Fragment: FLC CME DNA / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3')


Mass: 4562.000 Da / Num. of mol.: 2 / Fragment: FLC CME DNA / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 3.63 Å3/Da / Density % sol: 66.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M sodium HEPES pH 7.5, 15% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 8746 / % possible obs: 99.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 9.4
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 3.56 / Num. unique obs: 1271 / CC1/2: 0.995 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J9A

6j9a


Resolution: 3.102→49.591 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / Phase error: 23.01
RfactorNum. reflection% reflection
Rfree0.2568 446 5.1 %
Rwork0.2246 --
obs0.2263 8746 67.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.102→49.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 1218 0 0 3022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013199
X-RAY DIFFRACTIONf_angle_d1.1564555
X-RAY DIFFRACTIONf_dihedral_angle_d29.4071284
X-RAY DIFFRACTIONf_chiral_restr0.073493
X-RAY DIFFRACTIONf_plane_restr0.007378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1024-3.55130.2593350.2199734X-RAY DIFFRACTION18
3.5513-4.47380.26992010.23313376X-RAY DIFFRACTION84
4.4738-49.59780.24532100.21934190X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.24422.1871-0.33886.0068-5.03135.12430.0793-0.02160.09330.3568-0.22970.9224-0.514-0.39830.13720.5718-0.03740.30140.192-0.14710.54382.560130.6969-19.0277
22.3887-0.4061-1.69650.30540.37972.4853-0.0930.27920.2314-0.35550.1624-0.2443-0.41340.40390.18180.8142-0.19110.4030.36490.16390.568419.681831.2435-35.5248
31.5591-1.4142-0.26021.28540.2530.26330.00880.0639-0.0573-0.32640.1594-0.017-0.0649-0.0092-0.11631.0109-0.16690.05330.2880.09540.86873.917625.4508-31.8584
40.0002-0.0410.04075.1561-5.12855.1005-0.41530.51660.4053-0.98520.4870.96820.2511-0.4725-0.10911.03330.03220.03140.55670.0390.6719-0.838935.0774-36.0252
51.76510.82290.96451.88-0.10231.07110.108-0.12580.22020.3886-0.08560.0699-0.22010.00170.00590.6617-0.19280.17850.24920.10750.44429.889938.3034-24.3074
63.82481.42370.8058.77060.49035.05740.158-0.1010.37960.051-0.083-0.0794-0.9434-0.00670.05470.8550.01050.37920.154-0.03750.3869.109935.3307-21.4908
70.5127-0.5967-0.20772.85031.13770.4580.22750.1410.2243-0.5877-0.37980.1424-0.6599-0.1625-0.07591.75710.03460.58890.4731-0.070.797616.269930.1829-48.6901
80.24090.04930.10022.7993-2.83792.9663-0.03410.3291-0.2557-0.9651-0.2624-0.81220.5290.46820.61391.5422-0.04150.48710.59770.27240.824419.192833.4443-47.974
90.9546-0.5752-0.44790.34260.27120.21570.08710.0173-0.06430.028-0.0225-0.0238-0.06070.0925-0.0198-0.02170.32930.1884-0.03610.01890.4845-1.630311.3024-11.7529
101.2031-1.5404-1.84172.10412.86924.76420.1415-0.08450.2395-0.32990.0254-0.3375-0.79290.8915-0.17190.1153-0.07620.01280.21450.10210.36596.832917.9714-13.9602
113.90620.3703-3.25332.1715-0.94116.8108-0.1168-0.2533-0.1085-0.15570.18770.055-0.0922-0.0734-0.10780.2025-0.01460.15990.01180.04580.2643-1.168915.8475-9.6478
122.0915-0.25590.47625.1059-0.7232.0672-0.04660.22050.0063-0.5947-0.15450.089-0.22690.0061-0.05020.26170.0199-0.1650.00980.12720.33-3.783916.6514-20.3954
137.22266.54751.98258.5631.46082.3328-0.2642-0.6273-0.03340.09820.0702-0.3295-0.23610.26130.23660.60540.00180.38760.6024-0.12620.45986.733710.7956-19.6942
140.4715-0.54440.07710.76460.35251.45530.16230.1066-0.3791-0.0112-0.06550.24470.1786-0.130.20130.22570.00080.2304-0.1637-0.1190.8528-16.762318.9556-2.6282
150.71220.4939-0.02440.6287-0.37250.6540.0997-0.17010.1090.3582-0.14130.157-0.36090.0744-0.01340.3768-0.2340.2616-0.3311-0.01490.931-15.414915.6894-0.3121
160.8403-0.05150.23830.85412.12625.4476-0.38240.44720.2263-1.12040.26690.0215-0.87940.36560.09750.5698-0.2566-0.05570.2202-0.06750.19238.680839.6205-20.2219
171.3395-2.11-1.27295.10033.02181.7917-0.07920.43660.2965-0.7930.0823-0.0029-0.4131-0.06230.0151.2084-0.02380.12750.33670.07160.39486.702831.1719-40.7115
185.42270.29390.22150.8478-0.09852.01340.39280.18261.0893-0.2926-0.2558-0.9088-0.41950.2817-0.10541.0348-0.34260.21330.57290.14650.772117.458638.2168-34.2861
195.02693.8659-1.93082.9882-1.84629.25630.038-0.0365-0.2289-0.5292-0.0894-0.91350.3690.40750.07250.8909-0.07170.17880.44220.08461.042225.328331.773-30.0137
205.1611-3.2855-3.39453.26591.88412.7482-0.1355-0.2163-0.24220.0442-0.1288-0.0460.15050.30320.21640.4962-0.06090.17690.28510.20240.400314.462728.1143-23.1869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 212 through 217 )
2X-RAY DIFFRACTION2chain 'D' and (resid 218 through 237 )
3X-RAY DIFFRACTION3chain 'D' and (resid 238 through 246 )
4X-RAY DIFFRACTION4chain 'D' and (resid 247 through 252 )
5X-RAY DIFFRACTION5chain 'D' and (resid 253 through 259 )
6X-RAY DIFFRACTION6chain 'D' and (resid 260 through 271 )
7X-RAY DIFFRACTION7chain 'E' and (resid 1 through 15 )
8X-RAY DIFFRACTION8chain 'F' and (resid 1 through 15 )
9X-RAY DIFFRACTION9chain 'A' and (resid 163 through 205 )
10X-RAY DIFFRACTION10chain 'A' and (resid 206 through 211 )
11X-RAY DIFFRACTION11chain 'A' and (resid 212 through 237 )
12X-RAY DIFFRACTION12chain 'A' and (resid 238 through 259 )
13X-RAY DIFFRACTION13chain 'A' and (resid 260 through 273 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1 through 15 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 15 )
16X-RAY DIFFRACTION16chain 'D' and (resid 160 through 174 )
17X-RAY DIFFRACTION17chain 'D' and (resid 175 through 184 )
18X-RAY DIFFRACTION18chain 'D' and (resid 185 through 195 )
19X-RAY DIFFRACTION19chain 'D' and (resid 196 through 205 )
20X-RAY DIFFRACTION20chain 'D' and (resid 206 through 211 )

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