+Open data
-Basic information
Entry | Database: PDB / ID: 7n8w | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of ERI2 nuclease bound to rAMP | ||||||||||||||||||
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: 2.35 Å | ||||||||||||||||||
Authors | Thapar, R. / Arvai, A.S. / Tainer, J.A. | ||||||||||||||||||
Funding support | United States, 5items
| ||||||||||||||||||
Citation | Journal: To Be Published Title: Crystal structure of ERI2 nuclease bound to rAMP Authors: Thapar, R. / Arvai, A.S. / Tainer, J.A. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7n8w.cif.gz | 227.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7n8w.ent.gz | 151 KB | Display | PDB format |
PDBx/mmJSON format | 7n8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n8w_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7n8w_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7n8w_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 7n8w_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/7n8w ftp://data.pdbj.org/pub/pdb/validation_reports/n8/7n8w | HTTPS FTP |
-Related structure data
Related structure data | 4l83S S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.936361118806, 0.193294095175, -0.293027725581), (-0.0353982591461, -0.882482784683, -0.469010765321), (-0.34924893477, -0.428790773581, 0.833164842065)Vector: -51. ...NCS oper: (Code: given Matrix: (-0.936361118806, 0.193294095175, -0.293027725581), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#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 |
---|
-Non-polymers , 5 types, 14 molecules
#2: Chemical | ChemComp-AMP / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MN / | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.43 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 9% MPEG 2K, 1% saturated Magnesium Sulfate, 5% Ethylene glycol, 200 mM Imidazole Malate buffer pH 5.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
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: 2.35→50 Å / Num. obs: 19057 / % possible obs: 90.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 48.79 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: 0.104 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 2.35→2.39 Å / Num. unique obs: 1820 / Rrim(I) all: 0.55 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4l83 Resolution: 2.35→44.69 Å / SU ML: 0.2983 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 35.507 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→44.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.86165181966 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|