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Yorodumi- PDB-7lpz: Crystal structures and ribonuclease activity of the Flavivirus ho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lpz | ||||||||||||
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Title | Crystal structures and ribonuclease activity of the Flavivirus host factor ERI3 that is involved in viral RNA synthesis define the ERI subfamily of structure-specific 3-prime - 5-prime exoribonucleases | ||||||||||||
Components | ERI1 exoribonuclease 3 | ||||||||||||
Keywords | HYDROLASE / HYDROLASE METAL BINDING | ||||||||||||
Function / homology | Function and homology information exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / RNA binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||||||||
Authors | Thapar, R. / Andrew, A.S. / Tainer, J.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Crystal structures and ribonuclease activity of the Flavivirus host factor ERI3 that is involved in viral RNA synthesis define the ERI subfamily of structure-specific 3' - 5' exoribonucleases Authors: Thapar, R. / Arvai, A.S. / Tainer, J.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lpz.cif.gz | 233.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lpz.ent.gz | 155.6 KB | Display | PDB format |
PDBx/mmJSON format | 7lpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lpz_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 7lpz_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 7lpz_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 7lpz_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/7lpz ftp://data.pdbj.org/pub/pdb/validation_reports/lp/7lpz | HTTPS FTP |
-Related structure data
Related structure data | 7k05C 7lpyC 7lq0C 2xriS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.0120605054072, 0.115438158984, 0.993241448823), (0.205984769455, 0.971722321892, -0.115438312049), (-0.978480873069, 0.205984855235, -0.0120590402472)Vector: 47. ...NCS oper: (Code: given Matrix: (0.0120605054072, 0.115438158984, 0.993241448823), Vector: |
-Components
#1: Protein | Mass: 25068.066 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERI3, PINT1, PRNPIP, PRNPIP1 / Production host: Escherichia coli (E. coli) References: UniProt: O43414, Hydrolases; Acting on ester bonds #2: Chemical | #3: Chemical | ChemComp-SM / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.12 Å3/Da / Density % sol: 42.03 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 30% PEG 3350, 25% saturated KCl, 200 mM Imidazole / Malate buffer 8.0, 2.5 mM samarium (III) acetate, 18mM AMP, 3.3 mM N-{2-[4-(thiophen-2-yl)-1H-imidazol-2-yl]ethyl}-2,3-dihydro-1,4- ...Details: 30% PEG 3350, 25% saturated KCl, 200 mM Imidazole / Malate buffer 8.0, 2.5 mM samarium (III) acetate, 18mM AMP, 3.3 mM N-{2-[4-(thiophen-2-yl)-1H-imidazol-2-yl]ethyl}-2,3-dihydro-1,4-benzodioxine-2-carboxamide (from Life Chemicals) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→37.39 Å / Num. obs: 407820 / % possible obs: 99.4 % / Redundancy: 6.56 % / Biso Wilson estimate: 28.81 Å2 / CC1/2: 1 / Net I/σ(I): 22.42 |
Reflection shell | Resolution: 1.55→1.64 Å / Num. unique obs: 63859 / CC1/2: 0.631 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XRI Resolution: 1.55→37.39 Å / SU ML: 0.199 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.8326 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→37.39 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.533027182314 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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