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- PDB-4up7: Crystal structure of Entamoeba histolytica lysyl-tRNA synthetase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4up7 | ||||||
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Title | Crystal structure of Entamoeba histolytica lysyl-tRNA synthetase in complex with lysyl-adenylate | ||||||
![]() | LYSINE--TRNA LIGASE | ||||||
![]() | LIGASE / AMINOACYLATION | ||||||
Function / homology | ![]() ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA binding / mitochondrion / extracellular space ...ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA binding / mitochondrion / extracellular space / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bonnefond, L. / Nureki, O. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.4 KB | Display | ![]() |
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PDB format | ![]() | 187.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 694.7 KB | Display | ![]() |
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Full document | ![]() | 698.7 KB | Display | |
Data in XML | ![]() | 20.1 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4up8C ![]() 4up9C ![]() 4upaC ![]() 3bjuS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 87741.219 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-LAD / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: 8 Details: 50 MM HEPES PH 8.0, 50 MM NACL, 1 MM SPERMINE, 8% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→37.4 Å / Num. obs: 32784 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 22.8 % / Biso Wilson estimate: 76.48 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 22.2 % / Mean I/σ(I) obs: 1.8 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3BJU Resolution: 2.789→36.047 Å / SU ML: 0.4 / σ(F): 1.35 / Phase error: 25.17 / 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: 86.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.789→36.047 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: 181.8448 Å / Origin y: -63.8053 Å / Origin z: -15.4699 Å
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Refinement TLS group | Selection details: (CHAIN A AND RESSEQ 2:591) |