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Open data
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Basic information
Entry | Database: PDB / ID: 4koo | ||||||
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Title | Crystal Structure of WHY1 from Arabidopsis thaliana | ||||||
![]() | Single-stranded DNA-binding protein WHY1, chloroplastic | ||||||
![]() | DNA BINDING PROTEIN / Plant / Whirly / SINGLE-STRANDED DNA BINDING PROTEIN | ||||||
Function / homology | ![]() salicylic acid mediated signaling pathway / chloroplast nucleoid / systemic acquired resistance / DNA repair complex / regulation of telomere maintenance / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / chloroplast / defense response / single-stranded DNA binding ...salicylic acid mediated signaling pathway / chloroplast nucleoid / systemic acquired resistance / DNA repair complex / regulation of telomere maintenance / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / chloroplast / defense response / single-stranded DNA binding / chromosome, telomeric region / DNA repair / mRNA binding / regulation of DNA-templated transcription / DNA binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cappadocia, L. / Parent, J.S. / Brisson, N. / Sygusch, J. | ||||||
![]() | ![]() Title: A family portrait: structural comparison of the Whirly proteins from Arabidopsis thaliana and Solanum tuberosum. Authors: Cappadocia, L. / Parent, J.S. / Sygusch, J. / Brisson, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 278.4 KB | Display | ![]() |
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PDB format | ![]() | 230.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.4 KB | Display | ![]() |
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Full document | ![]() | 499.9 KB | Display | |
Data in XML | ![]() | 35.7 KB | Display | |
Data in CIF | ![]() | 51.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20007.902 Da / Num. of mol.: 4 / Fragment: UNP residues 74-241 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MES / #3: Chemical | ChemComp-NI / | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 5% PEG 3350, 0.2M Potassium Acetate, 0.1M MES pH5.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.88→50 Å / Num. all: 69860 / Num. obs: 69721 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.048 / Χ2: 1.058 / Net I/σ(I): 19.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.59 Å2 / Biso mean: 35.8517 Å2 / Biso min: 8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→30.276 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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