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- PDB-6ab2: Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ab2 | ||||||
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Title | Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with oClZLys | ||||||
![]() | Pyrrolysine--tRNA ligase | ||||||
![]() | TRANSLATION / aminoacyl-tRNA synthetase / non-natural amino acids | ||||||
Function / homology | ![]() pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yanagisawa, T. / Kuratani, M. / Yokoyama, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase. Authors: Yanagisawa, T. / Kuratani, M. / Seki, E. / Hino, N. / Sakamoto, K. / Yokoyama, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.9 KB | Display | ![]() |
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PDB format | ![]() | 106.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6aacC ![]() 6aadC ![]() 6aanC ![]() 6aaoC ![]() 6aapC ![]() 6aaqC ![]() 6aazC ![]() 6ab0C ![]() 6ab1C ![]() 6ab8C ![]() 6abkC ![]() 6ablC ![]() 6abmC ![]() 2zimS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 31346.982 Da / Num. of mol.: 1 / Mutation: Y306A, Y384F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pylS / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 286 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/9V6.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/9V6.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ATP / | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | The sequence reference Q8PWY1 (PYLS_METMA) is derived from a different strain (Methanosarcina mazei ...The sequence reference Q8PWY1 (PYLS_METMA) is derived from a different strain (Methanosarcina mazei Go1, TaxID 192952). Residue E444G is a natural mutation observed in PylRS gene from Methanosarcina mazei JCM 9314 genome. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.08 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Tris-HCl (pH 8.5), PEG 200, KCl, MgCl2, sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 53399 / % possible obs: 97.5 % / Redundancy: 7.6 % / Rpim(I) all: 0.021 / Rrim(I) all: 0.058 / Net I/σ(I): 34.5 |
Reflection shell | Resolution: 1.4→1.44 Å / Num. unique obs: 2623 / Rpim(I) all: 0.161 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2zim Resolution: 1.4→35.071 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 19.54 / 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: 1.4→35.071 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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