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- PDB-3g1z: Structure of IDP01693/yjeA, a potential t-RNA synthetase from Sal... -

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Basic information

Entry
Database: PDB / ID: 3g1z
TitleStructure of IDP01693/yjeA, a potential t-RNA synthetase from Salmonella typhimurium
ComponentsPutative lysyl-tRNA synthetase
KeywordsLIGASE / t-RNA synthetase / drug target / Salmonella typhimurium / nucleotide / Aminoacyl-tRNA synthetase / ATP-binding / Nucleotide-binding / Protein biosynthesis / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


protein-lysine lysylation / acid-ammonia (or amide) ligase activity / Ligases; Forming carbon-nitrogen bonds; Acid-ammonia (or amine) ligases (amide synthases) / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / ATP binding / cytosol
Similarity search - Function
Elongation factor P--(R)-beta-lysine ligase / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / Elongation factor P--(R)-beta-lysine ligase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSinger, A.U. / Evdokimova, E. / Kudritska, M. / Cuff, M.E. / Edwards, A.M. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Mol.Cell / Year: 2010
Title: PoxA, yjeK, and elongation factor P coordinately modulate virulence and drug resistance in Salmonella enterica.
Authors: Navarre, W.W. / Zou, S.B. / Roy, H. / Xie, J.L. / Savchenko, A. / Singer, A. / Edvokimova, E. / Prost, L.R. / Kumar, R. / Ibba, M. / Fang, F.C.
History
DepositionJan 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 12, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative lysyl-tRNA synthetase
B: Putative lysyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,20911
Polymers73,9102
Non-polymers1,3009
Water11,620645
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-71 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.901, 68.905, 73.270
Angle α, β, γ (deg.)90.00, 110.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative lysyl-tRNA synthetase / Lysine--tRNA ligase / LysRS / GX


Mass: 36954.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DIGESTED WITH TEV TO REMOVE THE N-TERMINAL HIS TAG / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: genX, poxA, STM4344, yjeA / Plasmid: p15TvLic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CODON PLUS RIPL / References: UniProt: Q9ZJ12, lysine-tRNA ligase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M Sodium/Potassium dihydrogen phosphate, 0.1 M HEPES, pH 7.5, 0.5 mM ATP and 0.3 mM MgCl2, cryoprotected in N-Paratone oil , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 26, 2008 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 56264 / Num. obs: 54044 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 20.05
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 3.82 / Num. unique all: 4784 / % possible all: 85.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Swiss-model (http://swissmodel.expasy.org/SWISS-MODEL.html) model using the input protein sequence

Resolution: 1.95→47.51 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.615 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.197 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 2339 5.1 %RANDOM
Rwork0.18112 ---
obs0.1841 43960 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.664 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5012 0 77 645 5734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215429
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9777402
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9845673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91323.865282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58815917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1121548
X-RAY DIFFRACTIONr_chiral_restr0.10.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024261
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22948
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23730
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2597
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7241.53376
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16725302
X-RAY DIFFRACTIONr_scbond_it1.99532293
X-RAY DIFFRACTIONr_scangle_it34.52095
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 191 -
Rwork0.212 3318 -
obs-3509 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42890.2646-0.01760.71470.01470.26960.0673-0.10380.03810.1163-0.0345-0.0506-0.0330.015-0.03270.0001-0.01640.0033-0.01740.0036-0.04796.02498.503-20.5215
20.45390.39450.27170.76040.07470.32430.0871-0.0911-0.08850.1298-0.07650.01520.0676-0.0618-0.0105-0.0044-0.02530.0146-0.01160.0147-0.0371-15.509-20.5653-21.0228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 325
2X-RAY DIFFRACTION2B5 - 325

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