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- PDB-4up9: Crystal structure of Entamoeba histolytica lysyl-tRNA synthetase ... -

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Basic information

Entry
Database: PDB / ID: 4up9
TitleCrystal structure of Entamoeba histolytica lysyl-tRNA synthetase in complex with ATP
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, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain ...Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / 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
ADENOSINE-5'-TRIPHOSPHATE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesENTAMOEBA HISTOLYTICA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.047 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
Revision 1.2Nov 26, 2014Group: Database references
Revision 1.3Dec 10, 2014Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

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Assembly

Deposited unit
A: LYSINE--TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2642
Polymers87,7571
Non-polymers5071
Water0
1
A: LYSINE--TRNA LIGASE
hetero molecules

A: LYSINE--TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,5294
Polymers175,5142
Non-polymers1,0142
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area10220 Å2
ΔGint-40.1 kcal/mol
Surface area44000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.551, 155.551, 92.926
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(DE3) ROSETTA / References: UniProt: C4M7X2, lysine-tRNA ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: 50 MM HEPES PH 8.0, 50 MM NACL, 7.5% PEG 4000, 1.2 MM SPERMINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1
DetectorType: ADSC Q270 / Detector: CCD / Date: Dec 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→43.9 Å / Num. obs: 24433 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Biso Wilson estimate: 79.01 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.8
Reflection shellResolution: 3.05→3.26 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.1 / % possible all: 96.3

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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: 3.047→40.431 Å / SU ML: 0.49 / σ(F): 1.35 / Phase error: 28.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 1237 5.1 %
Rwork0.2163 --
obs0.2186 24396 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.3 Å2
Refinement stepCycle: LAST / Resolution: 3.047→40.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4020 0 31 0 4051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054138
X-RAY DIFFRACTIONf_angle_d0.9085606
X-RAY DIFFRACTIONf_dihedral_angle_d13.311541
X-RAY DIFFRACTIONf_chiral_restr0.034626
X-RAY DIFFRACTIONf_plane_restr0.006723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.047-3.16890.38871420.33372446X-RAY DIFFRACTION95
3.1689-3.31310.37311610.31432574X-RAY DIFFRACTION100
3.3131-3.48770.28341410.26412547X-RAY DIFFRACTION100
3.4877-3.7060.27271390.24432588X-RAY DIFFRACTION100
3.706-3.99190.27751250.21442584X-RAY DIFFRACTION100
3.9919-4.39320.27191380.1932557X-RAY DIFFRACTION99
4.3932-5.02790.22351290.16762605X-RAY DIFFRACTION99
5.0279-6.33070.25871300.20642593X-RAY DIFFRACTION100
6.3307-40.43430.21111320.20142665X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -68.4181 Å / Origin y: 9.0039 Å / Origin z: -15.0563 Å
111213212223313233
T0.4974 Å2-0.0893 Å2-0.0911 Å2-0.7021 Å20.0039 Å2--0.4806 Å2
L0.3841 °2-0.2324 °2-0.0028 °2-3.677 °20.0035 °2--0.7551 °2
S-0.0968 Å °-0.107 Å °0.1044 Å °0.6438 Å °0.0953 Å °-0.7072 Å °-0.0274 Å °0.1289 Å °0.0434 Å °
Refinement TLS groupSelection details: ALL

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