+Open data
-Basic information
Entry | Database: PDB / ID: 6neo | ||||||
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Title | Crystal structure of PprA filament from Deinococcus radiodurans | ||||||
Components | DNA repair protein PprA | ||||||
Keywords | DNA BINDING PROTEIN / PROTEIN FIBRIL / DNA damage repair / Radiation induced / Genome segregation / Filament formation | ||||||
Function / homology | cellular response to desiccation / positive regulation of DNA ligation / cellular response to gamma radiation / double-stranded DNA binding / damaged DNA binding / DNA repair / DNA repair protein PprA Function and homology information | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 5.94 Å | ||||||
Authors | Szabla, R. / Junop, M.S. / Rok, M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: Crystal structure of PprA filament from Deinococcus radiodurans Authors: Szabla, R. / Junop, M.S. / Rok, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6neo.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6neo.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 6neo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6neo_validation.pdf.gz | 387.8 KB | Display | wwPDB validaton report |
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Full document | 6neo_full_validation.pdf.gz | 387.8 KB | Display | |
Data in XML | 6neo_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 6neo_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/6neo ftp://data.pdbj.org/pub/pdb/validation_reports/ne/6neo | HTTPS FTP |
-Related structure data
Related structure data | 6mc8S 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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Unit cell |
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-Components
#1: Protein | Mass: 29919.477 Da / Num. of mol.: 1 / Mutation: D180K, D184K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: pprA, DR_A0346 / Plasmid: pDEST-527 Details (production host): Gateway destination vector with TEV-protease cleavable N-terminal His tag Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32504 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.55 Å3/Da / Density % sol: 72.96 % / Description: long hexagonal-base prism |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1:1 4.9 mg/mL protein in 150 mM potassium chloride, 20 mM Tris, pH 8.0 + Morpheus II-FX96 (Molecular Dimensions) condition H2 - 40 mM polyamines (spermine tetrahydrochloride, spermidine ...Details: 1:1 4.9 mg/mL protein in 150 mM potassium chloride, 20 mM Tris, pH 8.0 + Morpheus II-FX96 (Molecular Dimensions) condition H2 - 40 mM polyamines (spermine tetrahydrochloride, spermidine trihydrochloride, 1,4-diaminobutane dihydrochloride, DL-ornithine monohydrochloride), 50% v/v Precipitant Mix 6 (25% w/v PEG4000, 40% w/v 1,2,6-hexanetriol), 0.1 M Buffer System 4 (Gly-Gly, AMPD) at pH 6.5. The drop was suspended over a 1.5 M ammonium sulfate dehydrating solution and incubated at 20 degrees C for about 5 months. Temp details: Temperature-controlled incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Nitrogen gas cryostream / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 5.94→67.53 Å / Num. obs: 1513 / % possible obs: 98.8 % / Redundancy: 13.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.261 / Rpim(I) all: 0.074 / Rrim(I) all: 0.278 / Χ2: 0.97 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 5.94→6.64 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 402 / CC1/2: 0.496 / Rpim(I) all: 0.565 / Χ2: 0.92 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6MC8 chain B Resolution: 5.94→50.0319 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5.94→50.0319 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 5.9395 Å |