+Open data
-Basic information
Entry | Database: PDB / ID: 3swm | ||||||
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Title | The NAC domain of ANAC019 in complex with DNA, gold derivative | ||||||
Components |
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Keywords | TRANSCRIPTION/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 | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.25 Å | ||||||
Authors | Welner, D. / Lo Leggio, L. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3swm.cif.gz | 315.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3swm.ent.gz | 255.2 KB | Display | PDB format |
PDBx/mmJSON format | 3swm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3swm_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
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Full document | 3swm_full_validation.pdf.gz | 493.9 KB | Display | |
Data in XML | 3swm_validation.xml.gz | 21 KB | Display | |
Data in CIF | 3swm_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/3swm ftp://data.pdbj.org/pub/pdb/validation_reports/sw/3swm | HTTPS FTP |
-Related structure data
Related structure data | 3swpC 4dulC 1ut7S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | 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 | | Mass: 8028.178 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: DNA chain | | Mass: 7948.129 Da / Num. of mol.: 1 / Source method: obtained synthetically #4: Chemical | ChemComp-AU / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.48 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.038 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.038 Å / Relative weight: 1 |
Reflection | Resolution: 4.25→46.203 Å / Num. all: 9600 / Num. obs: 9600 / % possible obs: 100 % / Observed criterion σ(F): 2 |
Reflection shell | Resolution: 4.25→4.45 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UT7 + B-DNA model Resolution: 4.25→46.203 Å / SU ML: 0.54 / σ(F): 1.33 / Phase error: 29.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 175.159 Å2 / ksol: 0.28 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 4.25→46.203 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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