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Yorodumi- PDB-4tqd: Crystal Structure of the C-terminal domain of IFRS bound with 3-i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tqd | ||||||
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Title | Crystal Structure of the C-terminal domain of IFRS bound with 3-iodo-L-Phe 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: 2.1429 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 | 4tqd.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tqd.ent.gz | 54.3 KB | Display | PDB format |
PDBx/mmJSON format | 4tqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tqd_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4tqd_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4tqd_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 4tqd_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/4tqd ftp://data.pdbj.org/pub/pdb/validation_reports/tq/4tqd | HTTPS FTP |
-Related structure data
Related structure data | 4q6gC 4tqfC 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, 130 molecules
#2: Chemical | #3: Chemical | ChemComp-ATP / | #4: Chemical | ChemComp-33S / | #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: 3.35 Å3/Da / Density % sol: 63.26 % |
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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: 0.9789 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→42.064 Å / Num. obs: 24274 / % possible obs: 99.8 % / Redundancy: 20 % / Net I/σ(I): 34.24 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZIM Resolution: 2.1429→42.064 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 19.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1429→42.064 Å
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Refine LS restraints |
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LS refinement shell |
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