+Open data
-Basic information
Entry | Database: PDB / ID: 6rci | |||||||||||||||
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Title | Crystal structure of REXO2 | |||||||||||||||
Components | Oligoribonuclease, mitochondrialOligonucleotidase | |||||||||||||||
Keywords | HYDROLASE / Mitochondria / Oligoribonuclease / REXO2 | |||||||||||||||
Function / homology | Function and homology information Mitochondrial RNA degradation / Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-DNA exonuclease activity / nucleotide metabolic process / nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / mitochondrial intermembrane space / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial matrix ...Mitochondrial RNA degradation / Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-DNA exonuclease activity / nucleotide metabolic process / nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / mitochondrial intermembrane space / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial matrix / focal adhesion / nucleolus / magnesium ion binding / mitochondrion / nucleus / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||||||||
Authors | Spahr, H. / Nicholls, T.J. / Larsson, N.G. / Gustafsson, C.M. | |||||||||||||||
Funding support | Germany, Sweden, 4items
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Citation | Journal: Mol.Cell / Year: 2019 Title: Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria. Authors: Nicholls, T.J. / Spahr, H. / Jiang, S. / Siira, S.J. / Koolmeister, C. / Sharma, S. / Kauppila, J.H.K. / Jiang, M. / Kaever, V. / Rackham, O. / Chabes, A. / Falkenberg, M. / Filipovska, A. / ...Authors: Nicholls, T.J. / Spahr, H. / Jiang, S. / Siira, S.J. / Koolmeister, C. / Sharma, S. / Kauppila, J.H.K. / Jiang, M. / Kaever, V. / Rackham, O. / Chabes, A. / Falkenberg, M. / Filipovska, A. / Larsson, N.G. / Gustafsson, C.M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rci.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rci.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 6rci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/6rci ftp://data.pdbj.org/pub/pdb/validation_reports/rc/6rci | HTTPS FTP |
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-Related 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: 20894.963 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: REXO2, SFN, SMFN, CGI-114 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 References: UniProt: Q9Y3B8, Hydrolases; Acting on ester bonds #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: 2.37 Å3/Da / Density % sol: 48.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 100 mM Hepes pH 7.0, 200 mM sodium malonate, and 20 % polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→22.74 Å / Num. obs: 51266 / % possible obs: 98.8 % / Redundancy: 3.428 % / Biso Wilson estimate: 39.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.108 / Χ2: 1.345 / Net I/σ(I): 8.47 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→22.74 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.185 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.152
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Displacement parameters | Biso max: 116.62 Å2 / Biso mean: 48.63 Å2 / Biso min: 17.79 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→22.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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