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- PDB-4up7: Crystal structure of Entamoeba histolytica lysyl-tRNA synthetase ... -

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Basic information

Entry
Database: PDB / ID: 4up7
TitleCrystal structure of Entamoeba histolytica lysyl-tRNA synthetase in complex with lysyl-adenylate
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'-[LYSYL-PHOSPHATE] / Lysine--tRNA ligase
Similarity search - Component
Biological speciesENTAMOEBA HISTOLYTICA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.789 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)88,2172
Polymers87,7411
Non-polymers4751
Water0
1
A: LYSINE--TRNA LIGASE
hetero molecules

A: LYSINE--TRNA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,4334
Polymers175,4822
Non-polymers9512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_745-x+2,-y-1,z1
Buried area10540 Å2
ΔGint-39.1 kcal/mol
Surface area44870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.765, 155.765, 95.292
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: 87741.219 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-LAD / ADENOSINE-5'-[LYSYL-PHOSPHATE]


Mass: 475.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N7O8P

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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: 8
Details: 50 MM HEPES PH 8.0, 50 MM NACL, 1 MM SPERMINE, 8% PEG 4000

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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: 2.8→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 shellResolution: 2.8→2.95 Å / Redundancy: 22.2 % / Mean I/σ(I) obs: 1.8 / % possible all: 96.9

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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: 2.789→36.047 Å / SU ML: 0.4 / σ(F): 1.35 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 1707 5.2 %
Rwork0.2053 --
obs0.2063 32754 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.2 Å2
Refinement stepCycle: LAST / Resolution: 2.789→36.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 0 32 0 4271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034363
X-RAY DIFFRACTIONf_angle_d0.8015895
X-RAY DIFFRACTIONf_dihedral_angle_d13.7371659
X-RAY DIFFRACTIONf_chiral_restr0.03654
X-RAY DIFFRACTIONf_plane_restr0.003759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7892-2.87130.4851160.38862441X-RAY DIFFRACTION95
2.8713-2.96390.35471390.31682611X-RAY DIFFRACTION100
2.9639-3.06980.31641440.25822577X-RAY DIFFRACTION100
3.0698-3.19260.28041380.25442597X-RAY DIFFRACTION100
3.1926-3.33780.31331360.25582578X-RAY DIFFRACTION100
3.3378-3.51370.22321530.22232601X-RAY DIFFRACTION100
3.5137-3.73360.20071310.20342586X-RAY DIFFRACTION100
3.7336-4.02150.2251490.18752598X-RAY DIFFRACTION100
4.0215-4.42560.20661660.17052566X-RAY DIFFRACTION100
4.4256-5.06450.17581590.15182596X-RAY DIFFRACTION100
5.0645-6.37490.23871620.20592599X-RAY DIFFRACTION100
6.3749-36.05050.18691140.20432697X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 181.8448 Å / Origin y: -63.8053 Å / Origin z: -15.4699 Å
111213212223313233
T0.4742 Å20.0939 Å20.0354 Å2-0.5922 Å2-0.131 Å2--0.4314 Å2
L2.9121 °21.9153 °2-0.0093 °2-1.7535 °2-0.0338 °2--0.3369 °2
S0.3055 Å °-0.6357 Å °0.6005 Å °0.3141 Å °-0.3649 Å °0.4565 Å °-0.0555 Å °-0.0471 Å °0.0952 Å °
Refinement TLS groupSelection details: (CHAIN A AND RESSEQ 2:591)

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