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Yorodumi- PDB-7r6o: Pyrrolysyl-tRNA synthetase from methanogenic archaeon ISO4-G1 (G1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r6o | |||||||||
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Title | Pyrrolysyl-tRNA synthetase from methanogenic archaeon ISO4-G1 (G1PylRS) | |||||||||
Components | Pyrrolysyl-tRNA synthetase PylS | |||||||||
Keywords | TRANSLATION / tRNA synthetases / tRNA-ligase / tRNA synthetases class II | |||||||||
Function / homology | Function and homology information tRNA aminoacylation / aminoacyl-tRNA ligase activity / tRNA binding / translation / ATP binding Similarity search - Function | |||||||||
Biological species | methanogenic archaeon mixed culture ISO4-G1 (environmental samples) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Frkic, R.L. / Huber, T. / Jackson, C.J. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 Title: Genetic Encoding of Cyanopyridylalanine for In-Cell Protein Macrocyclization by the Nitrile-Aminothiol Click Reaction. Authors: Abdelkader, E.H. / Qianzhu, H. / George, J. / Frkic, R.L. / Jackson, C.J. / Nitsche, C. / Otting, G. / Huber, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r6o.cif.gz | 291.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r6o.ent.gz | 190.7 KB | Display | PDB format |
PDBx/mmJSON format | 7r6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/7r6o ftp://data.pdbj.org/pub/pdb/validation_reports/r6/7r6o | HTTPS FTP |
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-Related structure data
Related structure data | 6jp2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30893.084 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) methanogenic archaeon mixed culture ISO4-G1 (environmental samples) Gene: AUP07_0651 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A126QV54 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 30% w/v PEG 4000, 100mM Tris-HCl (pH 9.0), 200mM lithium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→48.01 Å / Num. obs: 57200 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 44.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.063 / Rrim(I) all: 0.168 / Net I/σ(I): 6.7 / Num. measured all: 401958 / Scaling rejects: 26 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JP2 Resolution: 2.2→46.56 Å / SU ML: 0.3628 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.3116 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→46.56 Å
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Refine LS restraints |
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LS refinement shell |
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