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- PDB-4ch3: 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: 4ch3 | ||||||
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Title | Structure of pyrrolysyl-tRNA synthetase in complex with adenylated butyryl lysine | ||||||
![]() | PYRROLYSINE--TRNA LIGASE | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() pyrrolysine-tRNAPyl ligase / ![]() ![]() ![]() ![]() 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 | ![]() | 126.8 KB | Display | ![]() |
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PDB format | ![]() | 98 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ch4C ![]() 4ch5C ![]() 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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Unit cell |
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Components
#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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#2: Chemical | ChemComp-YLB / | ||||
#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | ChemComp-EDO / ![]() #5: Water | ChemComp-HOH / | ![]() Sequence details | FIRST 21 AMINO ACIDS DISORDERED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.69 % / Description: NONE |
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Crystal grow![]() | pH: 7.4 / Details: 0.1 M LIAC, 12% 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: Jul 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.28→38.44 Å / Num. obs: 20634 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.69 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.86 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4BWA Resolution: 2.28→38.44 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.026 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 49.551 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→38.44 Å
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Refine LS restraints |
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