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- PDB-6abk: 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: 6abk | ||||||
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Title | Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with TeocLys | ||||||
![]() | 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 | ![]() | 144.1 KB | Display | ![]() |
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PDB format | ![]() | 109.6 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 ![]() 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
#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, DU43_20175, DU67_18120 / Production host: ![]() ![]() ![]() References: UniProt: A0A0F8JXW8, UniProt: Q8PWY1*PLUS, pyrrolysine-tRNAPyl ligase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-ATP / | ![]() #4: Chemical | ChemComp-9VF / ( | #5: Water | ChemComp-HOH / | ![]() Sequence details | Residue E444G is a natural mutation observed in PylRS gene from Methanosarcina mazei JCM9314 genome. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.41 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Oct 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.58→50 Å / Num. obs: 38450 / % possible obs: 99.9 % / Redundancy: 5 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.076 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.58→1.62 Å / Num. unique obs: 1888 / Rpim(I) all: 0.205 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2zim Resolution: 1.58→34.987 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 18.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→34.987 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 122.5554 Å / Origin y: 29.9311 Å / Origin z: 27.9423 Å
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Refinement TLS group | Selection details: all |