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Yorodumi- PDB-4zds: Crystal Structure of core DNA binding domain of Arabidopsis Thali... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zds | ||||||
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Title | Crystal Structure of core DNA binding domain of Arabidopsis Thaliana Transcription Factor Ethylene-Insensitive 3 | ||||||
Components | Protein ETHYLENE INSENSITIVE 3 | ||||||
Keywords | TRANSCRIPTION ACTIVATOR / DNA binding domain Transcription factor | ||||||
Function / homology | Function and homology information regulation of L-ascorbic acid biosynthetic process / sugar mediated signaling pathway / response to ethylene / ethylene-activated signaling pathway / kinase binding / response to hypoxia / transcription cis-regulatory region binding / defense response to bacterium / DNA-binding transcription factor activity / regulation of DNA-templated transcription ...regulation of L-ascorbic acid biosynthetic process / sugar mediated signaling pathway / response to ethylene / ethylene-activated signaling pathway / kinase binding / response to hypoxia / transcription cis-regulatory region binding / defense response to bacterium / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.78 Å | ||||||
Authors | Song, J. / Zhu, C. / Zhang, X. / Wen, X. / Liu, L. / Peng, J. / Guo, H. / Yi, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Plos One / Year: 2015 Title: Biochemical and Structural Insights into the Mechanism of DNA Recognition by Arabidopsis ETHYLENE INSENSITIVE3. Authors: Song, J. / Zhu, C. / Zhang, X. / Wen, X. / Liu, L. / Peng, J. / Guo, H. / Yi, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zds.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zds.ent.gz | 93.4 KB | Display | PDB format |
PDBx/mmJSON format | 4zds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/4zds ftp://data.pdbj.org/pub/pdb/validation_reports/zd/4zds | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15350.781 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 174-306 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O24606 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 25% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→46.26 Å / Num. obs: 23591 / % possible obs: 96.63 % / Redundancy: 3.9 % / Net I/σ(I): 22.81 |
-Processing
Software |
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Refinement | Resolution: 1.78→46.26 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.833 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.883 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→46.26 Å
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Refine LS restraints |
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