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Open data
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Basic information
Entry | Database: PDB / ID: 3n1l | ||||||
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Title | Crystal Structure of a StWhy2-rcERE32 complex | ||||||
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![]() | DNA BINDING PROTEIN/DNA / Single-stranded DNA binding protein / Plant / Whirly / Protein-DNA complex / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() defense response / single-stranded DNA binding / DNA repair / regulation of DNA-templated transcription / mitochondrion / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cappadocia, L. / Brisson, N. / Sygusch, J. | ||||||
![]() | ![]() Title: Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair. Authors: Cappadocia, L. / Marechal, A. / Parent, J.S. / Lepage, E. / Sygusch, J. / Brisson, N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.4 KB | Display | ![]() |
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PDB format | ![]() | 38.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3n1hC ![]() 3n1iC ![]() 3n1jC ![]() 3n1kC ![]() 1l3aS 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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1 | ![]()
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Unit cell |
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Details | Authors state that the biological unit is a tetramer protein plus a 32-mer DNA molecule, as indicated as pentamer in remark 350. Please refer to remark 999 for more details on the sequences specificity of this crystal structure. |
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Components
#1: Protein | Mass: 20000.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: DNA chain | Mass: 2773.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Synthesis / References: ![]() |
#3: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE OF THE CRYSTALLIZED DNA IS A 32-MER OLIGONUCLEOTIDE WITH SEQUENCE ...THE SEQUENCE OF THE CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 47.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 21% PEG6000, 0.1M Tris, 2.0M LiCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2007 |
Radiation | Monochromator: Si 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 8763 / Num. obs: 8716 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 29.1 % / Biso Wilson estimate: 56.1 Å2 / Rsym value: 0.954 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 805 / Rsym value: 0.75 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1L3A Resolution: 2.35→41.667 Å / SU ML: 2.36 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.698 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→41.667 Å
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Refine LS restraints |
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LS refinement shell |
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