+Open data
-Basic information
Entry | Database: PDB / ID: 4bw9 | ||||||
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Title | PylRS Y306G, Y384F, I405R mutant in complex with AMP-PNP | ||||||
Components | PYRROLYSINE--TRNA LIGASE | ||||||
Keywords | LIGASE | ||||||
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: 2.35 Å | ||||||
Authors | Schneider, S. / Vrabel, M. / Gattner, M.J. / Fluegel, V. / Lopez-Carillo, V. / Carell, T. | ||||||
Citation | Journal: Chem.Bio.Chem. / Year: 2013 Title: Structural Insights Into Incorporation of Norbornene Amino Acids for Click Modification of Proteins Authors: Schneider, S. / Gattner, M.J. / Vrabel, M. / Flugel, V. / Lopez-Carrillo, V. / Prill, S. / Carell, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bw9.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bw9.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 4bw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/4bw9 ftp://data.pdbj.org/pub/pdb/validation_reports/bw/4bw9 | HTTPS FTP |
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-Related structure data
Related structure data | 4bwaC 1q7eS 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: 33338.137 Da / Num. of mol.: 1 / Fragment: SYNTHETASE DOMAIN, RESIDUES 185-454 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHANOSARCINA MAZEI (archaea) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase |
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-Non-polymers , 5 types, 52 molecules
#2: Chemical | #3: Chemical | ChemComp-ANP / | #4: Chemical | ChemComp-1PE / | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.53 % / Description: NONE |
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Crystal grow | Details: 0.1 M SODIUM ACETATE, 15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Nov 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→45 Å / Num. obs: 18610 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 8.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q7E Resolution: 2.35→38.29 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 10.389 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.173 / 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: 60.881 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→38.29 Å
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Refine LS restraints |
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