+Open data
-Basic information
Entry | Database: PDB / ID: 6mc6 | ||||||
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Title | Crystal structure of PprA filament from Deinococcus radiodurans | ||||||
Components | DNA repair protein PprA | ||||||
Keywords | DNA BINDING PROTEIN / DNA damage repair / Radiation induced / Genome segregation / Filment 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 R1 (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.747 Å | ||||||
Authors | Szabla, R. / Junop, M.S. / Wood, K. | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: Crystal structure of PprA from Deinococcus radiodurans Authors: Szabla, R. / Wood, K. / Junop, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mc6.cif.gz | 218.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mc6.ent.gz | 173.8 KB | Display | PDB format |
PDBx/mmJSON format | 6mc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/6mc6 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/6mc6 | HTTPS FTP |
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-Related structure data
Related structure data | 6bduSC 6mc8C S: Starting model for refinement C: citing same article (ref.) |
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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.: 2 / Mutation: D180K, D184K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans R1 (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 for bacterial expression; N-terminal hexa-His tag Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): DE3 / References: UniProt: O32504 #2: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 50.8 % / Description: long rectangular prism |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Protein at 4.5 mg/mL in 150 mM KCl, 20 mM Tris, pH 7.5 was mixed in 1:1 volume ratio with Wizard Classic 1 (Rigaku) #46 - a solution of 200 mM Lithium sulfate, 10% (w/v) PEG 8000 and 100 mM ...Details: Protein at 4.5 mg/mL in 150 mM KCl, 20 mM Tris, pH 7.5 was mixed in 1:1 volume ratio with Wizard Classic 1 (Rigaku) #46 - a solution of 200 mM Lithium sulfate, 10% (w/v) PEG 8000 and 100 mM Imidazole/ HCl at pH 8.0. The drop was suspended over a 1.5M Ammonium sulfate dehydrating solution and incubated for about 5 weeks. Temp details: Temperature-controlled incubation |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Nitrogen gas cryo-stream |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97928 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97928 Å / Relative weight: 1 |
Reflection | Resolution: 2.747→90.95 Å / Num. obs: 16992 / % possible obs: 99.7 % / Redundancy: 7.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.103 / Rrim(I) all: 0.217 / Χ2: 7.8 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.75→2.88 Å / Redundancy: 8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2181 / CC1/2: 0.355 / Χ2: 0.93 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BDU Resolution: 2.747→51.41 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.747→51.41 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -1.5819 Å / Origin y: 37.0496 Å / Origin z: -11.2146 Å
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Refinement TLS group | Selection details: all |