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- PDB-4ldx: Crystal structure of the DNA binding domain of arabidopsis thalia... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ldx | ||||||
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Title | Crystal structure of the DNA binding domain of arabidopsis thaliana auxin response factor 1 (ARF1) in complex with protomor-like sequence ER7 | ||||||
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![]() | TRANSCRIPTION/DNA / protein-dna complex / Transcription factor / promotor DNA / nucleus / TRANSCRIPTION-DNA complex | ||||||
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 | ![]() | 323.4 KB | Display | ![]() |
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PDB format | ![]() | 261.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.1 KB | Display | ![]() |
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Full document | ![]() | 464.7 KB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lduC ![]() 4ldvSC ![]() 4ldwC ![]() 4ldyC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 41182.504 Da / Num. of mol.: 2 / Fragment: DNA Binding Domain, UNP residues 1-355 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | | Mass: 6429.158 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The sequence resembles naturally occurring promotors and is known to bind ARF proteins #3: DNA chain | | Mass: 6456.200 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The sequence resembles naturally occurring promotors and is known to bind ARF proteins #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 nL complex (4 mg/mL ARF1) and 100 nL crystallization buffer (10% PEG 20K, Glycine pH 8.5, 7.5% propanediol), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→35 Å / Num. obs: 25033 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3622 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4LDV Resolution: 2.9→33.81 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.868 / SU B: 38.943 / SU ML: 0.328 / Cross valid method: THROUGHOUT / ESU R Free: 0.394 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.427 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→33.81 Å
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Refine LS restraints |
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