+Open data
-Basic information
Entry | Database: PDB / ID: 3n1h | ||||||
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Title | Crystal Structure of StWhy2 | ||||||
Components | StWhy2 | ||||||
Keywords | DNA BINDING PROTEIN / StWhy2 / Single-stranded DNA binding protein / Plant / Potato / Whirly | ||||||
Function / homology | Function and homology information defense response / single-stranded DNA binding / DNA repair / regulation of DNA-templated transcription / mitochondrion / DNA binding Similarity search - Function | ||||||
Biological species | Solanum tuberosum (potato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å | ||||||
Authors | Cappadocia, L. / Brisson, N. / Sygusch, J. | ||||||
Citation | Journal: Plant Cell / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n1h.cif.gz | 47.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n1h.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 3n1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/3n1h ftp://data.pdbj.org/pub/pdb/validation_reports/n1/3n1h | HTTPS FTP |
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-Related structure data
Related structure data | 3n1iC 3n1jC 3n1kC 3n1lC 1l3aS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20000.715 Da / Num. of mol.: 1 / Fragment: Whirly domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum tuberosum (potato) / Strain: Kennebec / Gene: StWhy2 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D9J034*PLUS | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 21% PEG1000, 0.1M MOPS, 0.4M NH4H2PO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.08 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2007 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 10213 / Num. obs: 10208 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 37.3 % / Biso Wilson estimate: 45.402 Å2 / Rsym value: 0.076 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 19.5 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 986 / Rsym value: 0.92 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1L3A Resolution: 2.201→49.622 Å / SU ML: 1.74 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.06 / 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: 56.228 Å2 / ksol: 0.341 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.11 Å2
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Refinement step | Cycle: LAST / Resolution: 2.201→49.622 Å
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Refine LS restraints |
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LS refinement shell |
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