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- PDB-6abl: 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: 6abl | ||||||
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Title | Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with oBrZLys | ||||||
![]() | Pyrrolysine--tRNA ligase | ||||||
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Function / homology | ![]() pyrrolysine-tRNAPyl ligase / ![]() ![]() ![]() ![]() 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 | ![]() | 149.2 KB | Display | ![]() |
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PDB format | ![]() | 113.6 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 ![]() 6ab2C ![]() 6ab8C ![]() 6abkC ![]() 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
#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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#2: Chemical | #3: Chemical | ChemComp-ATP / | ![]() #4: Chemical | ChemComp-9VL / ( | #5: Water | ChemComp-HOH / | ![]() 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. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.38 % |
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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: RAYONIX MX225-HS / Detector: CCD / Date: Jul 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.47→50 Å / Num. obs: 48022 / % possible obs: 98.9 % / Redundancy: 4.1 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.066 / Net I/σ(I): 33 |
Reflection shell | Resolution: 1.47→1.51 Å / Num. unique obs: 2369 / Rpim(I) all: 0.252 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2zim Resolution: 1.47→35.061 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 19.44 / 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: 1.47→35.061 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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