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- PDB-7xlj: The crystal structure of ORE1(ANAC092) NAC domain -

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Basic information

Entry
Database: PDB / ID: 7xlj
TitleThe crystal structure of ORE1(ANAC092) NAC domain
ComponentsNAC domain-containing protein 92
KeywordsTRANSCRIPTION / Transcription factor / plant protein / TRANSCRIPTION regulator
Function / homology
Function and homology information


floral organ senescence / positive regulation of age-related resistance / positive regulation of leaf senescence / regulation of seed germination / response to ethylene / lateral root development / leaf senescence / response to auxin / response to abscisic acid / response to salt ...floral organ senescence / positive regulation of age-related resistance / positive regulation of leaf senescence / regulation of seed germination / response to ethylene / lateral root development / leaf senescence / response to auxin / response to abscisic acid / response to salt / positive regulation of programmed cell death / stress-induced premature senescence / response to salt stress / response to hydrogen peroxide / positive regulation of DNA-binding transcription factor activity / regulation of gene expression / response to oxidative stress / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / protein homodimerization activity / nucleus
Similarity search - Function
NAC domain / NAC domain superfamily / No apical meristem (NAM) protein / NAC domain profile.
Similarity search - Domain/homology
NAC domain-containing protein 92
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsChun, I.S. / Kim, M.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
Citation
Journal: Plant Commun. / Year: 2023
Title: Structural basis of DNA binding by the NAC transcription factor ORE1, a master regulator of plant senescence.
Authors: Chun, I. / Kim, H.J. / Hong, S. / Kim, Y.G. / Kim, M.S.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Structure of ORESARA1_DNA Binding Domain at 2.45 angstroms resolution
Authors: Chun, I.S.
History
DepositionApr 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAC domain-containing protein 92
B: NAC domain-containing protein 92


Theoretical massNumber of molelcules
Total (without water)37,6012
Polymers37,6012
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-11 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.333, 73.761, 78.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein NAC domain-containing protein 92 / ANAC092 / AtNAC2 / AtNAC6 / Protein ORESARA 1


Mass: 18800.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NAC92, NAC2, NAC6, ORE1, At5g39610, MIJ24.11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FKA0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M tris pH 8.5, 7% PEG20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.45→36.88 Å / Num. obs: 15181 / % possible obs: 98.5 % / Redundancy: 6.9 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.048 / Χ2: 0.961 / Net I/σ(I): 26.58
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 1301 / CC1/2: 0.907 / CC star: 0.975 / Χ2: 0.722 / % possible all: 86.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data collection
HKL-2000data scaling
PHENIX1.17.1_3660phasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ULX

3ulx


Resolution: 2.45→36.88 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 750 4.95 %
Rwork0.217 --
obs0.2192 15143 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 0 8 2399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092463
X-RAY DIFFRACTIONf_angle_d1.0923324
X-RAY DIFFRACTIONf_dihedral_angle_d24.081897
X-RAY DIFFRACTIONf_chiral_restr0.057342
X-RAY DIFFRACTIONf_plane_restr0.007413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.640.37131340.31732622X-RAY DIFFRACTION92
2.64-2.910.33071500.2882885X-RAY DIFFRACTION100
2.91-3.330.31251500.26692891X-RAY DIFFRACTION100
3.33-4.190.27571510.2282940X-RAY DIFFRACTION100
4.19-36.880.23281650.18793055X-RAY DIFFRACTION100
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)
12.3257-0.9648-2.16511.7927-0.16132.96630.21241.22140.25210.48540.06060.51360.0303-1.5003-0.40230.774-0.08650.11591.0119-0.06640.866126.571513.017447.9201
26.4834-2.1795-1.68936.16741.05884.9942-0.18311.0654-1.0755-0.3723-0.25450.59340.6407-0.62730.44210.7176-0.0961-0.05770.868-0.10590.802836.561810.010535.4471
36.78323.33540.57863.8553-2.37753.3389-0.47432.39111.4145-1.25150.31270.494-0.2476-0.63740.13250.9484-0.05910.02070.96150.25320.8229.224929.477930.811
43.1016-0.4182-0.61194.2351-1.38531.7017-0.09270.74360.1229-0.4876-0.0993-0.3361-0.0585-0.52740.02550.8962-0.0568-0.07060.9090.07990.890434.879222.803233.1734
54.9113-1.0869-1.44723.4891-0.37622.30050.13280.61141.2411-0.0944-0.0679-0.4184-0.4414-0.3910.07310.7521-0.0868-0.00270.83130.19370.913645.22926.005735.1778
64.2774-0.8628-1.95336.88490.30873.3593-0.16920.9179-0.1525-0.62120.2187-0.51740.3706-0.0209-0.06020.7788-0.1004-0.08051.0329-0.01920.688444.982811.912932.8642
73.028-0.8377-1.79562.73332.74315.9023-0.2873-0.0275-0.35890.2603-0.42760.78250.0148-0.1740.75590.9882-0.03230.16250.8761-0.02790.944425.052218.703457.088
85.86480.74442.51953.46871.3275.1171-0.0031-1.1464-1.10651.359-0.7731-0.42131.641-0.13860.56241.7293-0.10660.09331.36790.37231.592829.11217.246871.1854
95.28722.38751.8442.4114-1.09254.1660.335-1.0456-0.58831.04080.3147-1.3340.23591.1442-0.58751.2866-0.0869-0.19931.6456-0.03081.273235.761520.565470.3854
104.7424-0.3232-1.06264.07181.98913.97150.0821-0.4044-0.22770.3438-0.112-0.857-0.47230.28040.15671.2072-0.1047-0.08170.9579-0.00541.361634.470431.842966.7603
118.1606-6.07492.99354.9303-3.76596.9809-0.4801-1.7534-1.27281.49580.56442.0465-0.31870.4482-0.11911.6051-0.07720.38811.68-0.16611.515215.962630.01271.8789
128.47340.1456-0.99084.9429-0.00654.9802-1.02430.72240.45240.06290.5398-1.71061.1450.03210.39731.12-0.11-0.09640.74790.07351.313236.924323.378964.2518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 98 )
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 145 )
6X-RAY DIFFRACTION6chain 'A' and (resid 146 through 170 )
7X-RAY DIFFRACTION7chain 'B' and (resid 17 through 43 )
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 63 )
9X-RAY DIFFRACTION9chain 'B' and (resid 64 through 99 )
10X-RAY DIFFRACTION10chain 'B' and (resid 100 through 149 )
11X-RAY DIFFRACTION11chain 'B' and (resid 150 through 162 )
12X-RAY DIFFRACTION12chain 'B' and (resid 163 through 170 )

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