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- PDB-3swp: ANAC019 NAC domain in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 3swp
TitleANAC019 NAC domain in complex with DNA
Components
  • NAC domain-containing protein 19
  • oligonucleotide forward
  • oligonucleotide reverse
KeywordsTRANSCRIPTION/DNA / mostly beta-sheet / transcription factor / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


system development / response to water deprivation / DNA-binding transcription factor activity / DNA binding / nucleus
Similarity search - Function
NAC domain / NAC domain superfamily / No apical meristem (NAM) protein / NAC domain profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / NAC domain-containing protein 19
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.113 Å
AuthorsWelner, D. / Lo Leggio, L.
CitationJournal: Biochem.J. / Year: 2012
Title: DNA binding by the plant-specific NAC transcription factors in crystal and solution: a firm link to WRKY and GCM transcription factors.
Authors: Welner, D.H. / Lindemose, S. / Grossmann, J.G. / Mollegaard, N.E. / Olsen, A.N. / Helgstrand, C. / Skriver, K. / Lo Leggio, L.
History
DepositionJul 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAC domain-containing protein 19
B: NAC domain-containing protein 19
C: NAC domain-containing protein 19
D: NAC domain-containing protein 19
E: oligonucleotide forward
F: oligonucleotide reverse


Theoretical massNumber of molelcules
Total (without water)97,2856
Polymers97,2856
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.140, 105.470, 175.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 17:76 or resseq 86:142 or resseq 153:163 )
211chain C and (resseq 17:76 or resseq 86:142 or resseq 153:163 )
112chain B and (resseq 8:37 or resseq 40:77 or resseq 86:141 or resseq 153:161 )
212chain D and (resseq 8:37 or resseq 40:77 or resseq 86:141 or resseq 153:161 )

NCS ensembles :
ID
1
2

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Components

#1: Protein
NAC domain-containing protein 19 / ANAC019 / Abscicic-acid-responsive NAC / ANAC


Mass: 20327.270 Da / Num. of mol.: 4 / Fragment: NAC domain (UNP residues 1-168)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NAC019, ANAC, At1g52890, F14G24.16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C932
#2: DNA chain oligonucleotide forward


Mass: 8028.178 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain oligonucleotide reverse


Mass: 7948.129 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.01 M magnesium sulfate, 0.05 M MES, pH 6.5, 0.5% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.038 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 16, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 4.113→29.966 Å / Num. all: 10433 / Num. obs: 10348 / % possible obs: 99.4 %
Reflection shellResolution: 4.113→4.4 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UT7 + B-DNA model

1ut7


Resolution: 4.113→29.966 Å / SU ML: 0.6 / σ(F): 1.99 / Phase error: 36.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.349 1035 10.02 %
Rwork0.2603 --
obs0.2688 10333 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 159.295 Å2 / ksol: 0.259 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--32.7247 Å20 Å2-0 Å2
2--60.8948 Å20 Å2
3----28.1701 Å2
Refinement stepCycle: LAST / Resolution: 4.113→29.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4601 1066 0 0 5667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155934
X-RAY DIFFRACTIONf_angle_d2.4848239
X-RAY DIFFRACTIONf_dihedral_angle_d23.8792236
X-RAY DIFFRACTIONf_chiral_restr0.107861
X-RAY DIFFRACTIONf_plane_restr0.01845
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1078X-RAY DIFFRACTIONPOSITIONAL
12C1078X-RAY DIFFRACTIONPOSITIONAL0.05
21B1109X-RAY DIFFRACTIONPOSITIONAL
22D1109X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1132-4.32940.44431390.36061250X-RAY DIFFRACTION95
4.3294-4.59980.3511470.31381317X-RAY DIFFRACTION100
4.5998-4.95350.34731460.26841313X-RAY DIFFRACTION100
4.9535-5.44930.32071460.24761307X-RAY DIFFRACTION100
5.4493-6.23160.37041490.25341340X-RAY DIFFRACTION100
6.2316-7.8280.37581510.2591359X-RAY DIFFRACTION100
7.828-29.96670.30951570.22671412X-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)
14.0802-6.3141-0.41133.8020.14-4.6957-0.73561.9971-0.9787-0.02580.2148-0.1110.3317-0.4050.541.2752-0.45990.04261.3267-0.26641.395320.3066-20.3716-35.0513
2-1.33170.56011.65247.66997.8924.0442-0.2296-0.9277-0.31182.59720.5028-1.18322.1878-0.5726-0.36172.32640.19240.08521.72640.68331.684325.037-18.9177-2.2684
35.6899-4.12044.70880.4297-2.425-0.48710.04970.71350.0983-0.93990.18-0.0949-0.5280.1405-0.26181.3372-0.06120.05271.46720.14622.101914.269523.8041-50.1344
45.20389.1681.32539.6201-4.69894.20480.4462-1.2101-0.04712.6308-0.7313-1.0063-1.8409-0.58530.00572.52580.29680.02351.7699-0.1492.097310.528220.7519-17.5756
56.446-1.48651.20041.11632.30890.971-1.4581.00711.15690.6604-0.2067-0.7593-2.2251-1.78020.60824.1745-0.1294-0.69891.95940.22441.865917.70570.2759-13.0975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E or chain F

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