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Yorodumi- PDB-4upa: Crystal structure of Entamoeba histolytica lysyl-tRNA synthetase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4upa | ||||||
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Title | Crystal structure of Entamoeba histolytica lysyl-tRNA synthetase in complex with AMPPNP | ||||||
Components | LYSINE--TRNA LIGASE | ||||||
Keywords | LIGASE / AMINOACYLATION | ||||||
Function / homology | Function and homology information lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ENTAMOEBA HISTOLYTICA (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 Å | ||||||
Authors | Bonnefond, L. / Nureki, O. | ||||||
Citation | Journal: FEBS Lett. / Year: 2014 Title: Crystal Structures of Entamoeba Histolytica Lysyl-tRNA Synthetase Reveal Conformational Changes Upon Lysine Binding and a Specific Helix Bundle Domain. Authors: Bonnefond, L. / Castro De Moura, M. / Ribas De Pouplana, L. / Nureki, O. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4upa.cif.gz | 227 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4upa.ent.gz | 179.5 KB | Display | PDB format |
PDBx/mmJSON format | 4upa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/4upa ftp://data.pdbj.org/pub/pdb/validation_reports/up/4upa | HTTPS FTP |
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-Related structure data
Related structure data | 4up7C 4up8C 4up9C 3bjuS 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
#1: Protein | Mass: 87757.242 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ENTAMOEBA HISTOLYTICA (eukaryote) / Plasmid: PET-30 EK/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41(DE3) ROSETTA / References: UniProt: C4M7X2, lysine-tRNA ligase |
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#2: Chemical | ChemComp-ANP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.6 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 50 MM HEPES PH 8.0, 50 MM NACL, 7.5% PEG 4000, 1.2 MM SPERMINE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 |
Detector | Type: ADSC Q270 / Detector: CCD / Date: Dec 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→39.2 Å / Num. obs: 29250 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Biso Wilson estimate: 84.21 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.9→3.1 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.1 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BJU Resolution: 2.901→38.683 Å / SU ML: 0.46 / σ(F): 1.35 / Phase error: 24.82 / Stereochemistry target values: ML
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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: 80.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.901→38.683 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 147.0406 Å / Origin y: 126.8564 Å / Origin z: 15.5773 Å
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Refinement TLS group | Selection details: ALL |