+Open data
-Basic information
Entry | Database: PDB / ID: 7pvm | ||||||
---|---|---|---|---|---|---|---|
Title | NMR structure of the C. thermophilum Xrn2 zinc finger | ||||||
Components | 5'-3' exoribonuclease | ||||||
Keywords | RNA BINDING PROTEIN / Zinc finger | ||||||
Function / homology | Function and homology information 5'-3' RNA exonuclease activity / DNA-templated transcription termination / mRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleic acid binding / nucleus Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Overbeck, J.H. / Sprangers, R. / Wurm, J.P. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2022 Title: Observation of conformational changes that underlie the catalytic cycle of Xrn2. Authors: Overbeck, J.H. / Stelzig, D. / Fuchs, A.L. / Wurm, J.P. / Sprangers, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7pvm.cif.gz | 212.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7pvm.ent.gz | 179.9 KB | Display | PDB format |
PDBx/mmJSON format | 7pvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/7pvm ftp://data.pdbj.org/pub/pdb/validation_reports/pv/7pvm | HTTPS FTP |
---|
-Related structure data
Related structure data | 7opkC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 3310.810 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0008830 / Production host: Escherichia coli (E. coli) References: UniProt: G0S058, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
---|---|
#2: Chemical | ChemComp-ZN / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Type: solution Contents: 25 mM HEPES, 125 mM NaCl, 0.03 % NaN3, 95% H2O/5% D2O Label: sample1 / Solvent system: 95% H2O/5% D2O | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||
Sample conditions | Ionic strength: 125 mM / Label: conditions1 / pH: 7.3 / Pressure: 1 atm / Temperature: 288 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: medoid | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |