+Open data
-Basic information
Entry | Database: PDB / ID: 6rcl | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of REXO2-D199A-AA | |||||||||||||||
Components |
| |||||||||||||||
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) synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | |||||||||||||||
Authors | Spahr, H. / Nicholls, T.J. / Larsson, N.G. / Gustafsson, C.M. | |||||||||||||||
Funding support | Germany, Sweden, 4items
| |||||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6rcl.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6rcl.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 6rcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/6rcl ftp://data.pdbj.org/pub/pdb/validation_reports/rc/6rcl | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20850.953 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: RNA chain | | Mass: 613.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.66 % / Mosaicity: 0.12 ° |
---|---|
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 | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 1, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.97→41.98 Å / Num. obs: 27363 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 48.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.028 / Rrim(I) all: 0.082 / Net I/σ(I): 13.4 / Num. measured all: 221998 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→41.98 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.164 / SU Rfree Cruickshank DPI: 0.16
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 158.37 Å2 / Biso mean: 58.14 Å2 / Biso min: 31.31 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.97→41.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.97→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
|