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- PDB-4ch5: Structure of pyrrolysyl-tRNA synthetase in complex with adenylate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ch5 | ||||||
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Title | Structure of pyrrolysyl-tRNA synthetase in complex with adenylated propionyl lysine | ||||||
![]() | PYRROLYSINE--TRNA LIGASE | ||||||
![]() | LIGASE / NON-NATURAL AMINO ACID / PYRROLYSINE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Fluegel, V. / Vrabel, M. / Schneider, S. | ||||||
![]() | ![]() Title: Structural Basis for the Site-Specific Incorporation of Lysine Derivatives Into Proteins. Authors: Flugel, V. / Vrabel, M. / Schneider, 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 | ![]() | 127.3 KB | Display | ![]() |
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PDB format | ![]() | 98.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 723.8 KB | Display | ![]() |
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Full document | ![]() | 724.8 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ch3C ![]() 4ch4C ![]() 4ch6C ![]() 4bwaS 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: 33416.227 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 185-454 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 97 molecules ![](data/chem/img/YLP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-YLP / ( | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-POP / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | FIRST 21 AMINO ACIDS DISORDERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.5 % / Description: NONE |
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Crystal grow | pH: 7.4 / Details: 0.1 M LIAC, 14% PEG3350, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→42.3 Å / Num. obs: 22651 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / Redundancy: 10.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.96 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BWA Resolution: 2.2→42.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.96 / SU B: 6.877 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. RESIDUES 380-383 DISORDERED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.825 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→42.3 Å
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Refine LS restraints |
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