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Yorodumi- PDB-6f3h: Crystal structure of Dss1 exoribonuclease active site mutant D477... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f3h | ||||||
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Title | Crystal structure of Dss1 exoribonuclease active site mutant D477N from Candida glabrata | ||||||
Components |
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Keywords | HYDROLASE / 3' to 5' exoribonuclease RNA degradation mitochondria | ||||||
Function / homology | Function and homology information mitochondrial degradosome / mitochondrial RNA catabolic process / exoribonuclease II activity / RNA nuclease activity / mitochondrion / RNA binding Similarity search - Function | ||||||
Biological species | Candida glabrata (fungus) Escherichia coli BL21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.703 Å | ||||||
Authors | Razew, M. / Nowak, E. / Nowotny, M. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components. Authors: Razew, M. / Warkocki, Z. / Taube, M. / Kolondra, A. / Czarnocki-Cieciura, M. / Nowak, E. / Labedzka-Dmoch, K. / Kawinska, A. / Piatkowski, J. / Golik, P. / Kozak, M. / Dziembowski, A. / Nowotny, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f3h.cif.gz | 619.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f3h.ent.gz | 520.1 KB | Display | PDB format |
PDBx/mmJSON format | 6f3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/6f3h ftp://data.pdbj.org/pub/pdb/validation_reports/f3/6f3h | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 95343.742 Da / Num. of mol.: 2 / Mutation: D477N Source method: isolated from a genetically manipulated source Details: 69 N-terminal truncation was introduced in the full length protein Source: (gene. exp.) Candida glabrata (fungus) Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65 Gene: CAGL0M07051g / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q6FJE0 #2: RNA chain | | Mass: 1899.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RNA molecule co-purified with the protein / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Variant: RIL #3: RNA chain | | Mass: 1875.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RNA molecule co-purified with the protein / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Variant: RIL #4: Chemical | #5: 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: 3.17 Å3/Da / Density % sol: 61.25 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES monohydrate (pH 6.5) and 6% (w/v) PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29.211 Å / Num. obs: 129398 / % possible obs: 98.8 % / Redundancy: 4.6 % / Rrim(I) all: 0.173 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.7→2.77 Å / Rrim(I) all: 0.938 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.703→29.211 Å / Cross valid method: FREE R-VALUE / σ(F): 2.3 / Phase error: 30.31 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.703→29.211 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: -10.7182 Å / Origin y: 60.2468 Å / Origin z: 40.2839 Å
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Refinement TLS group | Selection details: all |