[English] 日本語
Yorodumi- PDB-1ntg: Crystal Structure of the EMAP II-like Cytokine Released from huma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ntg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the EMAP II-like Cytokine Released from human tyrosyl-tRNA Synthetase | ||||||
Components | Tyrosyl-tRNA synthetase | ||||||
Keywords | LIGASE / beta barrel | ||||||
Function / homology | Function and homology information interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process ...interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process / extracellular space / RNA binding / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Yang, X.-L. / Skene, R.J. / Mcree, D.E. / Schimmel, P. | ||||||
Citation | Journal: Helv.Chim.Acta / Year: 2003 Title: Crystal Structure of an EMAP-II-like Cytokine Released from a human tRNA Synthetase Authors: Yang, X.-L. / Liu, J. / Skene, R.J. / McRee, D.E. / Schimmel, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ntg.cif.gz | 142.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ntg.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ntg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/1ntg ftp://data.pdbj.org/pub/pdb/validation_reports/nt/1ntg | HTTPS FTP |
---|
-Related structure data
Related structure data | 1fl0S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19124.049 Da / Num. of mol.: 4 / Fragment: C-TyrRS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YARS / Plasmid: PET20b / Production host: Escherichia coli (E. coli) / References: UniProt: P54577, tyrosine-tRNA ligase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 52.85 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: ammonium sulfate, Sodium phosphate mono-basic, potassium phosphate di-basic, acetone, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 279K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 30, 2001 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→20 Å / Num. all: 39281 / Num. obs: 39281 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 2.21→2.29 Å / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.8 / % possible all: 83.7 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å |
Reflection shell | *PLUS % possible obs: 83.7 % |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EMAP II structure (PDB 1FL0) Resolution: 2.21→20 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→20 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |