[English] 日本語
Yorodumi- PDB-4h3s: The Structure of Glutaminyl-tRNA Synthetase from Saccharomyces Ce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h3s | ||||||
---|---|---|---|---|---|---|---|
Title | The Structure of Glutaminyl-tRNA Synthetase from Saccharomyces Cerevisiae | ||||||
Components | Glutamine-tRNA ligase | ||||||
Keywords | LIGASE / Rossmann Fold / Appended domain / tRNA synthetase / Beta barrel anticodon binding domain / Pseudo zinc finger motif | ||||||
Function / homology | Function and homology information glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / sequence-specific mRNA binding / mRNA binding / mitochondrion / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacementSAD / Resolution: 2.15 Å | ||||||
Authors | Snell, E.H. / Grant, T.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: The Structure of Yeast Glutaminyl-tRNA Synthetase and Modeling of Its Interaction with tRNA. Authors: Grant, T.D. / Luft, J.R. / Wolfley, J.R. / Snell, M.E. / Tsuruta, H. / Corretore, S. / Quartley, E. / Phizicky, E.M. / Grayhack, E.J. / Snell, E.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4h3s.cif.gz | 395.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4h3s.ent.gz | 327.4 KB | Display | PDB format |
PDBx/mmJSON format | 4h3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h3s_validation.pdf.gz | 471 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4h3s_full_validation.pdf.gz | 473.7 KB | Display | |
Data in XML | 4h3s_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 4h3s_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/4h3s ftp://data.pdbj.org/pub/pdb/validation_reports/h3/4h3s | HTTPS FTP |
-Related structure data
Related structure data | 1gtsS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 94117.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: BCY123 / Gene: GLN4, O3601, YOR168W / References: UniProt: P13188, glutamine-tRNA ligase |
---|
-Non-polymers , 7 types, 463 molecules
#2: Chemical | ChemComp-ZN / | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-BR / | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-ACT / #7: Chemical | ChemComp-DTT / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.38 % |
---|---|
Crystal grow | Temperature: 287.15 K / Method: batch under oil / pH: 7.5 Details: 3.5 micro L of protein solution (13.9 mg/ml protein in 200mM NaCl, 5% (v/v) glycerol, 2mM DTT, 0.025% (w/v) NaN3, 20mM HEPES buffer, pH 7.5) with 2.0 micro L of precipitant solution (50mM ...Details: 3.5 micro L of protein solution (13.9 mg/ml protein in 200mM NaCl, 5% (v/v) glycerol, 2mM DTT, 0.025% (w/v) NaN3, 20mM HEPES buffer, pH 7.5) with 2.0 micro L of precipitant solution (50mM NH4Br, 50mM KC2H3O2, 100mM HEPES, pH 7.5 and 20%(w/v) PEG 20K, Batch under oil, temperature 287.15K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.1696 Å | ||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 12, 2008 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.1696 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.15→76.47 Å / Num. obs: 70276 / % possible obs: 99.86 % / Observed criterion σ(I): 3 / Redundancy: 11.2 % / Biso Wilson estimate: 33.55 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 23.3 | ||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: molecular replacementSAD Starting model: PDB ENTRY 1GTS Resolution: 2.15→52.495 Å / SU ML: 0.16 / σ(F): 1.33 / Phase error: 19.04 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→52.495 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|