[English] 日本語
Yorodumi- PDB-4q6g: Crystal Structure of the C-terminal domain of AcKRS-1 bound with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q6g | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the C-terminal domain of AcKRS-1 bound with N-acetyl-lysine and ADPNP | ||||||
Components | Pyrrolysine--tRNA ligase | ||||||
Keywords | LIGASE / tRNA synthetase / tRNA / amino acids | ||||||
Function / homology | Function and homology information pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanosarcina mazei (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Eiler, D.R. / Kavran, J. / Steitz, T.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Polyspecific pyrrolysyl-tRNA synthetases from directed evolution. Authors: Guo, L.T. / Wang, Y.S. / Nakamura, A. / Eiler, D. / Kavran, J.M. / Wong, M. / Kiessling, L.L. / Steitz, T.A. / O'Donoghue, P. / Soll, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4q6g.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4q6g.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 4q6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/4q6g ftp://data.pdbj.org/pub/pdb/validation_reports/q6/4q6g | HTTPS FTP |
---|
-Related structure data
Related structure data | 4tqdC 4tqfC 2q7gS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30812.246 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 188-454) / Mutation: L226V,L270I,Y271F,L274A,C313F,S382M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88 Gene: pylS, MM_1445 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-ANP / | ||||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-ALY / | #5: Water | ChemComp-HOH / | Nonpolymer details | BIOCHEMICAL EVIDENCE SUGGESTS THAT THE ACETYL END OF LIGAND D ALY 2005 MAY NOT BE AS WELL-ORDERED ...BIOCHEMICA | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.35 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50 mM Tris, pH 8.0, 23% PEG2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.248→90.909 Å / Num. all: 21278 / Num. obs: 21010 / % possible obs: 98.7 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 7.5 % / Rsym value: 0.048 / Net I/σ(I): 41.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Q7G Resolution: 2.25→90.909 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.679 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.752 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→90.909 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|