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- PDB-4up8: Crystal structure of Entamoeba histolytica lysyl-tRNA synthetase ... -

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Basic information

Entry
Database: PDB / ID: 4up8
TitleCrystal structure of Entamoeba histolytica lysyl-tRNA synthetase apo form
ComponentsLYSINE--TRNA LIGASE
KeywordsLIGASE / 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
Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain ...Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesENTAMOEBA HISTOLYTICA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.896 Å
AuthorsBonnefond, L. / Nureki, O.
CitationJournal: 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
DepositionJun 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references / Refinement description
Revision 1.2Nov 26, 2014Group: Database references
Revision 1.3Dec 10, 2014Group: Database references
Revision 1.4Jan 21, 2015Group: Atomic model
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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 viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSINE--TRNA LIGASE


Theoretical massNumber of molelcules
Total (without water)87,7571
Polymers87,7571
Non-polymers00
Water00
1
A: LYSINE--TRNA LIGASE

A: LYSINE--TRNA LIGASE


Theoretical massNumber of molelcules
Total (without water)175,5142
Polymers175,5142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_865-x+3,-y+1,z1
Buried area8970 Å2
ΔGint-43 kcal/mol
Surface area51950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.483, 156.483, 93.554
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein LYSINE--TRNA LIGASE / LYSYL-TRNA SYNTHETASE


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 ROSETTA / References: UniProt: C4M7X2, lysine-tRNA ligase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.6 % / Description: NONE
Crystal growpH: 7.5 / Details: 100 MM HEPES PH 7.5, 10% PEG 6000, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→34.5 Å / Num. obs: 29106 / % possible obs: 99.8 % / Observed criterion σ(I): 0.9 / Redundancy: 6.2 % / Biso Wilson estimate: 83.01 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.2
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 0.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BJU

3bju


Resolution: 2.896→34.541 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 26.9 / Stereochemistry target values: ML / Details: RESIDUES 303 TO 369 WERE MODELLED AS POLYALANINES
RfactorNum. reflection% reflection
Rfree0.2506 1406 4.8 %
Rwork0.2164 --
obs0.218 29095 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.8 Å2
Refinement stepCycle: LAST / Resolution: 2.896→34.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 0 0 4448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054535
X-RAY DIFFRACTIONf_angle_d1.0586139
X-RAY DIFFRACTIONf_dihedral_angle_d13.6021673
X-RAY DIFFRACTIONf_chiral_restr0.041698
X-RAY DIFFRACTIONf_plane_restr0.007800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8956-2.99910.4081450.37712700X-RAY DIFFRACTION99
2.9991-3.11910.33321360.32162768X-RAY DIFFRACTION100
3.1191-3.26090.30821490.2782762X-RAY DIFFRACTION100
3.2609-3.43270.31431510.26962729X-RAY DIFFRACTION100
3.4327-3.64750.29971340.23272789X-RAY DIFFRACTION100
3.6475-3.92880.26231420.22172766X-RAY DIFFRACTION100
3.9288-4.32350.21791210.19052781X-RAY DIFFRACTION100
4.3235-4.94760.2141340.17412794X-RAY DIFFRACTION100
4.9476-6.22750.23981520.21512768X-RAY DIFFRACTION100
6.2275-34.54320.21271420.19182832X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 164.3634 Å / Origin y: 84.5322 Å / Origin z: 26.3722 Å
111213212223313233
T1.0225 Å20.1201 Å2-0.4302 Å2-1.7465 Å2-0.3026 Å2--1.4809 Å2
L5.0563 °2-4.8787 °2-2.6333 °2-2 °22.0003 °2--9.5548 °2
S0.2065 Å °-3.6294 Å °-7.287 Å °8.9205 Å °4.9551 Å °-5.6767 Å °1.592 Å °2.1859 Å °0.8117 Å °
Refinement TLS groupSelection details: (CHAIN A AND RESSEQ -3:583)

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