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Open data
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Basic information
Entry | Database: PDB / ID: 5yzz | ||||||
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Title | AtVAL1 B3 domain in complex with 13bp-DNA | ||||||
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![]() | TRANSCRIPTION/DNA / transcriptional factor / Val1 / B3 domain / DNA complex / FLC / plant / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() response to sucrose / response to abscisic acid / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / mitochondrion / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, B.X. / Zhang, M.M. | ||||||
![]() | ![]() Title: Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana. Authors: Wu, B.X. / Zhang, M.M. / Su, S.C. / Liu, H.H. / Gan, J.H. / Ma, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53 KB | Display | ![]() |
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PDB format | ![]() | 34.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.1 KB | Display | ![]() |
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Full document | ![]() | 440.6 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 8.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yzySC ![]() 5z00C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3981.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 3959.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Protein | Mass: 14194.220 Da / Num. of mol.: 1 / Fragment: B3 domain, DNA binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 30% (w/v) PEG 5000 MME, 0.1M Tris base/Hydrochloric acid pH 8.0, 0.2M Lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→74.97 Å / Num. obs: 9191 / % possible obs: 99.5 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 2.58→2.67 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YZY Resolution: 2.58→30 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.893 / SU B: 13.293 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.547 / ESU R Free: 0.308 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.338 Å2
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Refinement step | Cycle: 1 / Resolution: 2.58→30 Å
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Refine LS restraints |
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