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- PDB-9or6: Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans -
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Open data
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Basic information
Entry | Database: PDB / ID: 9or6 | ||||||
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Title | Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans | ||||||
![]() | DNA repair protein PprA | ||||||
![]() | DNA BINDING PROTEIN / PprA / Deinococcus / Deinococcus radiodurans / D. radiodurans / DNA repair / Genome reassembly / self-assembly / protein filament | ||||||
Function / homology | cellular response to desiccation / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / double-stranded DNA binding / damaged DNA binding / DNA repair / SPERMIDINE / DNA repair protein PprA![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Szabla, R. / Junop, M.S. / Wood, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Self-assembly of PprA from D.radiodurans Authors: Szabla, R. / Junop, M.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.4 KB | Display | ![]() |
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PDB format | ![]() | 86.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.7 KB | Display | ![]() |
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Full document | ![]() | 452 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9om8C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29731.230 Da / Num. of mol.: 2 / Mutation: D180K, D184K Source method: isolated from a genetically manipulated source Details: 1-8 deletion of PprA from D.radiodurans with D180K/D184K mutation Source: (gene. exp.) ![]() Strain: R1 / Gene: pprA, DR_A0346 / Plasmid: pMJ5666 Details (production host): pDEST-527-based expression plasmid Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % / Description: long and thin hexagonal-based prisms |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 1.5 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. | Protein solution: 5.0 mg/mL PprA (168 ...Details: 1.5 ul of protein solution was mixed with 1.0 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution. | Protein solution: 5.0 mg/mL PprA (168 uM), 43bp dsDNA (101 uM), 150mM KCl, 20mM Tris, pH 7.5, 1 mM MgCl2. | Crystallization solution (Molecular Dimensions - Morpheus 2 #94): 10 mM Spermine tetrahydrochloride, 10 mM Spermidine trihydrochloride, 10 mM 1,4 Diaminobutane dihydrochloride, 10 mM DL Ornithine monohydrochloride 0.1M Gly-Gly, AMPD, pH 8.5, 13% w/v PEG 4000, 21% w/v 1,2,6 Hexanetriol. | Well solution: 2.0 M Ammonium sulfate. PH range: 7.5-8.5 / Temp details: Temperature-controlled incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Nitrogen cryo-stream / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 13, 2019 / Details: CMCF-ID optics setup |
Radiation | Monochromator: CMCF-ID default optics (Feb 2019) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→90.774 Å / Num. obs: 13352 / % possible obs: 96.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 51.01 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.069 / Rrim(I) all: 0.13 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.904→2.954 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 633 / CC1/2: 0.756 / Rpim(I) all: 0.417 / Rrim(I) all: 0.61 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→90.77 Å
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Refine LS restraints |
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LS refinement shell |
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