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Yorodumi- PDB-8ke4: PylRS C-terminus domain mutant bound with D-3-bromophenylalanine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ke4 | ||||||||||||
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Title | PylRS C-terminus domain mutant bound with D-3-bromophenylalanine and AMPNP | ||||||||||||
Components | Pyrrolysine--tRNA ligase | ||||||||||||
Keywords | LIGASE / tRNA Synthetase | ||||||||||||
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: 1.75050958755 Å | ||||||||||||
Authors | Weng, J.H. / Tsai, M.D. / Wang, Y.S. | ||||||||||||
Funding support | Taiwan, 3items
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Citation | Journal: Front Genet / Year: 2023 Title: Rational design of the genetic code expansion toolkit for in vivo encoding of D-amino acids. Authors: Jiang, H.K. / Weng, J.H. / Wang, Y.H. / Tsou, J.C. / Chen, P.J. / Ko, A.A. / Soll, D. / Tsai, M.D. / Wang, Y.S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ke4.cif.gz | 86 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ke4.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ke4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ke4_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ke4_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ke4_validation.xml.gz | 15 KB | Display | |
Data in CIF | 8ke4_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/8ke4 ftp://data.pdbj.org/pub/pdb/validation_reports/ke/8ke4 | HTTPS FTP |
-Related structure data
Related structure data | 8ke1C 8ke2C 8ke3C 8ke5C 8ke6C 2zceS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Methanosarcina mazei (archaea) / Gene: pylS, DU43_20175, DU67_18120 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F8JXW8, pyrrolysine-tRNAPyl ligase | ||||||
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#2: Chemical | ChemComp-ANP / | ||||||
#3: Chemical | #4: Chemical | ChemComp-FXF / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES buffer pH 7.5, 10% PEG 8000, 10% Ethylene Glycerol |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 27, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→28.2 Å / Num. obs: 45530 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 24.3372328819 Å2 / Rpim(I) all: 0.017 / Rrim(I) all: 0.056 / Net I/σ(I): 55.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZCE Resolution: 1.75050958755→28.1702948531 Å / SU ML: 0.151687980204 / Cross valid method: FREE R-VALUE / σ(F): 1.38114917239 / Phase error: 18.3268843451 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: 30.2227081296 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75050958755→28.1702948531 Å
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Refine LS restraints |
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LS refinement shell |
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