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Yorodumi- PDB-4tqf: Crystal Structure of the C-terminal domain of IFRS bound with 2-(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tqf | ||||||
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Title | Crystal Structure of the C-terminal domain of IFRS bound with 2-(5-bromothienyl)-L-Ala and ATP | ||||||
Components | Pyrrolysine--tRNA ligase | ||||||
Keywords | LIGASE / Amino Acyl-tRNA Synthetases / Archaeal Proteins / Evolution / Molecular / Genetic Code / Substrate Specificity | ||||||
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: 2.7143 Å | ||||||
Authors | Nakamura, A. / O'Donoghue, P. / Soll, D. | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tqf.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tqf.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 4tqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tqf_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4tqf_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4tqf_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 4tqf_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/4tqf ftp://data.pdbj.org/pub/pdb/validation_reports/tq/4tqf | HTTPS FTP |
-Related structure data
Related structure data | 4q6gC 4tqdC 2zimS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33399.219 Da / Num. of mol.: 1 / Mutation: N346S, C348I 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 / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus RIL (DE3) / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase |
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-Non-polymers , 5 types, 68 molecules
#2: Chemical | #3: Chemical | ChemComp-ATP / | #4: Chemical | ChemComp-33W / | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: Hepes, MgCl2, PEG3350 / PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9202 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9202 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→38.204 Å / Num. obs: 12071 / % possible obs: 99.8 % / Redundancy: 20 % / Net I/σ(I): 39.6 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7.2_869) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZIM Resolution: 2.7143→38.204 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 21.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.949 Å2 / ksol: 0.324 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7143→38.204 Å
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Refine LS restraints |
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LS refinement shell |
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