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Yorodumi- PDB-6wre: Crystal structure of mouse DXO in complex with 5'-OH RNA substrat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wre | ||||||
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Title | Crystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ion | ||||||
Components |
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Keywords | HYDROLASE / 5'-OH / RNA / cap | ||||||
Function / homology | Function and homology information RNA NAD+-cap (NAD+-forming) hydrolase activity / RNA destabilization / NAD-cap decapping / mRNA 5'-diphosphatase activity / nucleic acid metabolic process / nuclear mRNA surveillance / 5'-3' exonuclease activity / nuclear-transcribed mRNA catabolic process / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides ...RNA NAD+-cap (NAD+-forming) hydrolase activity / RNA destabilization / NAD-cap decapping / mRNA 5'-diphosphatase activity / nucleic acid metabolic process / nuclear mRNA surveillance / 5'-3' exonuclease activity / nuclear-transcribed mRNA catabolic process / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleotide binding / mRNA binding / magnesium ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Doamekpor, S.K. / Tong, L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: A novel 5'-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes. Authors: Doamekpor, S.K. / Gozdek, A. / Kwasnik, A. / Kufel, J. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wre.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wre.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 6wre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wre_validation.pdf.gz | 759.5 KB | Display | wwPDB validaton report |
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Full document | 6wre_full_validation.pdf.gz | 764.7 KB | Display | |
Data in XML | 6wre_validation.xml.gz | 17 KB | Display | |
Data in CIF | 6wre_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/6wre ftp://data.pdbj.org/pub/pdb/validation_reports/wr/6wre | HTTPS FTP |
-Related structure data
Related structure data | 4j7lS 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: 43132.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dxo, Dom3z, Ng6 / Production host: Escherichia coli (E. coli) References: UniProt: O70348, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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#2: RNA chain | Mass: 1824.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5'-OH / Source: (synth.) Homo sapiens (human) |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-U3P / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→49.83 Å / Num. obs: 29081 / % possible obs: 96 % / Redundancy: 1.99 % / Biso Wilson estimate: 42.125 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.072 / Χ2: 1.108 / Net I/σ(I): 8.91 / Num. measured all: 110559 / Scaling rejects: 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J7L Resolution: 2→49.83 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.56 Å2 / Biso mean: 42.1002 Å2 / Biso min: 23.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→49.83 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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