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Yorodumi- PDB-4ch5: Structure of pyrrolysyl-tRNA synthetase in complex with adenylate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ch5 | ||||||
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Title | Structure of pyrrolysyl-tRNA synthetase in complex with adenylated propionyl lysine | ||||||
Components | PYRROLYSINE--TRNA LIGASE | ||||||
Keywords | LIGASE / NON-NATURAL AMINO ACID / PYRROLYSINE | ||||||
Function / homology | Function and homology information pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | METHANOSARCINA MAZEI (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Fluegel, V. / Vrabel, M. / Schneider, S. | ||||||
Citation | Journal: Plos One / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ch5.cif.gz | 127.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ch5.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ch5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ch5_validation.pdf.gz | 723.8 KB | Display | wwPDB validaton report |
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Full document | 4ch5_full_validation.pdf.gz | 724.8 KB | Display | |
Data in XML | 4ch5_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4ch5_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/4ch5 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/4ch5 | HTTPS FTP |
-Related structure data
Related structure data | 4ch3C 4ch4C 4ch6C 4bwaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) METHANOSARCINA MAZEI (archaea) / Strain: GO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase |
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-Non-polymers , 5 types, 97 molecules
#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: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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