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- PDB-4dul: ANAC019 NAC domain crystal form IV -

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Basic information

Entry
Database: PDB / ID: 4dul
TitleANAC019 NAC domain crystal form IV
ComponentsNAC domain-containing protein 19
KeywordsTRANSCRIPTION / transcription factor / DNA binding domain
Function / homology
Function and homology information


response to water deprivation / DNA-binding transcription factor activity / DNA binding / nucleus
Similarity search - Function
NAC domain / NAC domain / NAC domain superfamily / No apical meristem (NAM) protein / NAC domain profile. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Beta Complex / Mainly Beta
Similarity search - Domain/homology
NAC domain-containing protein 19
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLo Leggio, L. / Helgstrand, C. / Welner, D. / Olsen, A.N. / Skriver, K.
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
DepositionFeb 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAC domain-containing protein 19
B: NAC domain-containing protein 19


Theoretical massNumber of molelcules
Total (without water)39,5612
Polymers39,5612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-12 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.082, 69.162, 75.950
Angle α, β, γ (deg.)90.00, 97.38, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 7 - 163 / Label seq-ID: 10 - 166

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 19780.664 Da / Num. of mol.: 2 / Fragment: NAC domain (UNP residues 1-163)
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4-6 mg/mL protein, precipitant: 12.5% PEG4000, 5% glycerol, 0.1 M malic acid/imidazole buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.087 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 2, 2004
RadiationMonochromator: bent Si(111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.087 Å / Relative weight: 1
ReflectionResolution: 3→75.32 Å / Num. all: 8549 / Num. obs: 8454 / % possible obs: 98.9 % / Redundancy: 3.7 % / Rsym value: 0.053 / Net I/σ(I): 25.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.392 / % possible all: 91.3

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UT7

1ut7


Resolution: 3→19.943 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.854 / SU B: 57.158 / SU ML: 0.46 / Cross valid method: THROUGHOUT / ESU R Free: 0.566 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.34211 359 4.6 %RANDOM
Rwork0.25366 ---
obs0.25745 7431 93.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.016 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å2-4.62 Å2
2---7.55 Å20 Å2
3---4.72 Å2
Refinement stepCycle: LAST / Resolution: 3→19.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 0 0 2079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022148
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.821.9562895
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4925238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43623.4100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.00915373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2411511
X-RAY DIFFRACTIONr_chiral_restr0.1270.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211600
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRms dev position (Å)Weight position
11A81X-RAY DIFFRACTION0.350.05
12B81X-RAY DIFFRACTION0.350.05
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 31 -
Rwork0.334 481 -
obs--85.76 %
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)
16.09192.2671.632710.16821.70194.0366-0.14080.24460.0917-0.31710.2527-0.8335-0.34040.2753-0.11180.27180.0260.26030.5563-0.06070.3359.690321.43494.1631
20.3293-1.1918-0.08285.19711.32448.3151-0.1817-0.0902-0.10370.8961-0.32510.3532-0.36260.20820.50681.2784-0.0656-0.36680.6717-0.06580.917912.80427.559434.0758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 163
2X-RAY DIFFRACTION2B7 - 163

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