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- PDB-8p5q: Structure of an ALOG domain from Arabidopsis thaliana in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8p5q | ||||||
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Title | Structure of an ALOG domain from Arabidopsis thaliana in complex with DNA | ||||||
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![]() | DNA BINDING PROTEIN / Transcription factor / ALOG domain / Arabidopsis thaliana / protein-DNA complex | ||||||
Function / homology | ![]() organ boundary specification between lateral organs and the meristem / petal development / specification of petal number / post-embryonic plant morphogenesis / maintenance of shoot apical meristem identity / mRNA transcription / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zubieta, C. / Nanao, M.H. / Rieu, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of an ALOG domain from Arabidopsis thaliana in complex with DNA Authors: Rieu, P. / Lucas, J. / Thevenon, E. / Dumas, R. / Beretta, V. / Caselli, F. / Franchini, E. / Caporali, E. / Kater, M. / Zubieta, C. / Nanao, M.H. / Gregis, V. / Parcy, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.9 KB | Display | ![]() |
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PDB format | ![]() | 80.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 827.7 KB | Display | ![]() |
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Full document | ![]() | 828 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14914.967 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 5188.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#3: DNA chain | Mass: 5223.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 3 types, 54 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.99 Å3/Da / Density % sol: 69.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.6M Ammonium sulfate, 0.1 M Hepes, 0.1M NaCl / PH range: 7-8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 25, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→67.57 Å / Num. obs: 43011 / % possible obs: 99.8 % / Redundancy: 7 % / CC1/2: 1 / Rrim(I) all: 0.04 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.14→2.2 Å / Redundancy: 7 % / Num. unique obs: 3138 / CC1/2: 0.325 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→49.69 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -10.8606 Å / Origin y: 18.5962 Å / Origin z: 14.2126 Å
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Refinement TLS group | Selection details: all |