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Open data
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Basic information
Entry | Database: PDB / ID: 3n1j | ||||||
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Title | Crystal structure of a StWhy2-dT32 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.3 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 ![]() 3n1kC ![]() 3n1lC ![]() 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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2 | ![]()
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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: 2692.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Synthesis |
#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: 2.14 Å3/Da / Density % sol: 47.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% PEG6000, 0.1M Tris, 1.2M 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: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. all: 6196 / Num. obs: 6188 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.1 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.118 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 605 / Rsym value: 0.87 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1L3A Resolution: 2.65→38.197 Å / SU ML: 2.53 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.05 / 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: 48.914 Å2 / ksol: 0.307 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→38.197 Å
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Refine LS restraints |
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LS refinement shell |
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