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Yorodumi- PDB-8dqh: Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dqh | |||||||||
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Title | Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus engineered for acridone amino acid (RS1) bound to ATP and acridone after 24 hours of crystal growth | |||||||||
Components | AA_TRNA_LIGASE_II domain-containing protein | |||||||||
Keywords | LIGASE / Genetic code expansion / Methanomethylophilus alvus / pyrrolysyl-tRNA synthetase / acridone | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Candidatus Methanomethylophilus alvus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | |||||||||
Authors | Gottfried-Lee, I. / Karplus, P.A. / Mehl, R.A. / Cooley, R.B. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2022 Title: Structures of Methanomethylophilus alvus Pyrrolysine tRNA-Synthetases Support the Need for De Novo Selections When Altering the Substrate Specificity. Authors: Gottfried-Lee, I. / Perona, J.J. / Karplus, P.A. / Mehl, R.A. / Cooley, R.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dqh.cif.gz | 320.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dqh.ent.gz | 262.3 KB | Display | PDB format |
PDBx/mmJSON format | 8dqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/8dqh ftp://data.pdbj.org/pub/pdb/validation_reports/dq/8dqh | HTTPS FTP |
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-Related structure data
Related structure data | 8dqgC 8dqiC 8dqjC 6jp2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules DA
#1: Protein | Mass: 30690.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Methanomethylophilus alvus (archaea) Gene: BKD89_05515 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G3IHP7 |
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-Non-polymers , 6 types, 476 molecules
#2: Chemical | #3: Chemical | ChemComp-T7Q / ( | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.84 Å3/Da / Density % sol: 56.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: PEG 3350, Sodium citrate tribasic dihydrate, magnesium chloride PH range: 5.0-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.52→45.44 Å / Num. obs: 105102 / % possible obs: 100 % / Redundancy: 14.2 % / Biso Wilson estimate: 23.66 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.02 / Rrim(I) all: 0.074 / Net I/σ(I): 20.4 / Num. measured all: 1496426 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
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: 1.52→45.44 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.66 Å2 / Biso mean: 35.5107 Å2 / Biso min: 15.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.52→45.44 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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