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- PDB-6ly3: PylRS C-terminus domain mutant bound with 3-Benzothienyl-L-alanin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ly3 | ||||||||||||
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Title | PylRS C-terminus domain mutant bound with 3-Benzothienyl-L-alanine and AMPNP | ||||||||||||
![]() | Pyrrolysine--tRNA ligase | ||||||||||||
![]() | LIGASE / tRNA Synthetase | ||||||||||||
Function / homology | ![]() pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Weng, J.H. / Tsai, M.D. / Wang, Y.S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues. Authors: Jiang, H.K. / Wang, Y.H. / Weng, J.H. / Kurkute, P. / Li, C.L. / Lee, M.N. / Chen, P.J. / Tseng, H.W. / Tsai, M.D. / Wang, Y.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 | ![]() | 131.1 KB | Display | ![]() |
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PDB format | ![]() | 92.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ly6C ![]() 6ly7C ![]() 6lyaC ![]() 6lybC ![]() 2zceS S: Starting model for refinement C: citing same article ( |
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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: 31999.602 Da / Num. of mol.: 1 / Fragment: C-terminus domain / Mutation: N346G,C348Q,V401G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A0F8JXW8, UniProt: Q8PWY1*PLUS, pyrrolysine-tRNAPyl ligase | ||||||
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#2: Chemical | ChemComp-ANP / | ||||||
#3: Chemical | #4: Chemical | ChemComp-4OG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES, 10% PEG 8000, 10% Ethylene Glycerol |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 |
Reflection | Resolution: 1.8958→38.463 Å / Num. obs: 35849 / % possible obs: 99.77 % / Redundancy: 11.3 % / Biso Wilson estimate: 30.3947927499 Å2 / Rpim(I) all: 0.02 / Rrim(I) all: 0.068 / Net I/σ(I): 36.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3499 / Rpim(I) all: 0.226 / Rrim(I) all: 0.735 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZCE Resolution: 1.8959014841→38.4629946681 Å / SU ML: 0.217725866964 / Cross valid method: FREE R-VALUE / σ(F): 1.3764791465 / Phase error: 19.8178998942 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.3724953184 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8959014841→38.4629946681 Å
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Refine LS restraints |
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LS refinement shell |
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