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- PDB-8dqg: Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dqg | |||||||||
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Title | Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus engineered for acridone amino acid (RS1) bound to AMPPNP and acridone | |||||||||
![]() | AA_TRNA_LIGASE_II domain-containing protein | |||||||||
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Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gottfried-Lee, I. / Karplus, P.A. / Mehl, R.A. / Cooley, R.B. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 397.2 KB | Display | ![]() |
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PDB format | ![]() | 314.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8dqhC ![]() 8dqiC ![]() 8dqjC ![]() 6jp2S C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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 / Mutation: N166A V168G W239C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BKD89_05515 / Production host: ![]() ![]() ![]() |
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-Non-polymers , 6 types, 519 molecules ![](data/chem/img/ANP.gif)
![](data/chem/img/T7Q.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/T7Q.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-T7Q / ( | #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GOL / | ![]() #6: Chemical | ChemComp-PEG / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.75 % |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||
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![]() | |||||||||||||||||||||||||||
Reflection | Resolution: 1.49→45.47 Å / Num. obs: 111755 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 22.54 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.019 / Rrim(I) all: 0.07 / Net I/σ(I): 20.1 / Num. measured all: 1445259 / Scaling rejects: 50 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 11.6 %
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6JP2 Resolution: 1.49→45.47 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.8 / 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: 93.37 Å2 / Biso mean: 33.2627 Å2 / Biso min: 15.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.49→45.47 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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