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- PDB-4ldy: Crystal structure of the DNA binding domain of the G245A mutant o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ldy | ||||||
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Title | Crystal structure of the DNA binding domain of the G245A mutant of arabidopsis thaliana auxin reponse factor 1 | ||||||
![]() | Auxin response factor 1 | ||||||
![]() | TRANSCRIPTION / Transcription factor / DNA binding / nucleus | ||||||
Function / homology | ![]() leaf senescence / response to auxin / cell death / auxin-activated signaling pathway / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boer, D.R. / Freire-Rios, A. / van den Berg, W.M.A. / Weijers, D. / Coll, M. | ||||||
![]() | ![]() Title: Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors. Authors: Boer, D.R. / Freire-Rios, A. / van den Berg, W.A. / Saaki, T. / Manfield, I.W. / Kepinski, S. / Lopez-Vidrieo, I. / Franco-Zorrilla, J.M. / de Vries, S.C. / Solano, R. / Weijers, D. / Coll, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 276.9 KB | Display | ![]() |
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PDB format | ![]() | 226.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.7 KB | Display | ![]() |
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Full document | ![]() | 443.8 KB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 35.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lduC ![]() 4ldvSC ![]() 4ldwC ![]() 4ldxC C: citing same article ( S: Starting model for refinement |
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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: Protein | Mass: 41093.391 Da / Num. of mol.: 2 / Fragment: DNA Binding Domain, UNP residues 1-355 / Mutation: G245A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.75 l of 13 mg/ml Arf1dbd-g245a +0.75 l crystallization buffer (100 mM bis-tris-propane pH 7.0, 0.7 M succinic acid), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→71.7 Å / Num. obs: 38764 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5641 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4LDV Resolution: 2.3→63.91 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.446 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.231 / 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: 60.556 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→63.91 Å
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Refine LS restraints |
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