+Open data
-Basic information
Entry | Database: PDB / ID: 7n8v | ||||||||||||||||||
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Title | Crystal structure of free ERI2 nuclease | ||||||||||||||||||
Components | ERI1 exoribonuclease 2 | ||||||||||||||||||
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 / nucleic acid binding / Hydrolases; Acting on ester bonds / zinc ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||||||||
Authors | Thapar, R. / Arvai, A.S. / Tainer, J.A. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: To Be Published Title: Crystal structure of free ERI2 nuclease 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 | 7n8v.cif.gz | 214.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n8v.ent.gz | 150.4 KB | Display | PDB format |
PDBx/mmJSON format | 7n8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n8v_validation.pdf.gz | 451.2 KB | Display | wwPDB validaton report |
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Full document | 7n8v_full_validation.pdf.gz | 452.7 KB | Display | |
Data in XML | 7n8v_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 7n8v_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/7n8v ftp://data.pdbj.org/pub/pdb/validation_reports/n8/7n8v | HTTPS FTP |
-Related structure data
Related structure data | 4l83S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.938544172593, 0.17419431996, -0.297978480741), (-0.0149121459388, -0.882965399522, -0.469201162775), (-0.344836865771, -0.435922518505, 0.831299641444)Vector: 8. ...NCS oper: (Code: given Matrix: (-0.938544172593, 0.17419431996, -0.297978480741), Vector: |
-Components
#1: Protein | Mass: 29951.580 Da / Num. of mol.: 2 / Fragment: exonuclease domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERI2, EXOD1, KIAA1504 / Production host: Escherichia coli (E. coli) References: UniProt: A8K979, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.09 Å3/Da / Density % sol: 41.03 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 15% MPEG 2K, 5% saturated MgSO4, 200 mM 5.6 Imidazole / Malate buffer, 5% Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11583 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11583 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 24036 / % possible obs: 82.1 % / Redundancy: 4 % / Biso Wilson estimate: 36.01 Å2 Details: The number provided for unique reflections observed in data collection is that found after merging Friedel pairs. The number recorded for refinement counts the individual Friedel mates separately Rrim(I) all: 0.112 / Net I/σ(I): 32.4 |
Reflection shell | Resolution: 2.1→2.14 Å / Num. unique obs: 1953 / Rrim(I) all: 0.583 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4l83 Resolution: 2.1→44.41 Å / SU ML: 0.2482 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 39.3391 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.41 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.81709297999 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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