+Open data
-Basic information
Entry | Database: PDB / ID: 4pqz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of swt1 C-terminal domain from yeast | ||||||
Components | Transcriptional protein SWT1Transcription (biology) | ||||||
Keywords | TRANSCRIPTION / HEPN like fold | ||||||
Function / homology | Function and homology information nuclear mRNA surveillance of mRNP export / RNA endonuclease activity / transcription elongation by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Peng, S.X. / Gao, Z.Q. / Liu, Q.S. / Dong, Y.H. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2014 Title: High-resolution crystal structure reveals a HEPN domain at the C-terminal region of S. cerevisiae RNA endonuclease Swt1. Authors: Peng, S. / Zhou, K. / Wang, W. / Gao, Z. / Dong, Y. / Liu, Q. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4pqz.cif.gz | 72.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4pqz.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 4pqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/4pqz ftp://data.pdbj.org/pub/pdb/validation_reports/pq/4pqz | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19645.986 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 312-458) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SWT1, YOR166C, O3595 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q12104 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.93 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M sodium acetate, 2 M sodium formate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 10, 2013 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 8495 / Num. obs: 8407 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 61.89 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 5.99 / Num. unique all: 420 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SEMET DERIVATIVE OF L379M MUTANT Resolution: 2.3→28.322 Å / SU ML: 0.51 / σ(F): 1.34 / Phase error: 28.99 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.562 Å2 / ksol: 0.349 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→28.322 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|