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- PDB-3pny: Structure of Glutamyl-tRNA synthetase from Mycobacterium tubercul... -

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Basic information

Entry
Database: PDB / ID: 3pny
TitleStructure of Glutamyl-tRNA synthetase from Mycobacterium tuberculosis in space group P21
ComponentsGlutamyl-tRNA synthetase
KeywordsLIGASE / non-discriminating glutamyl-trna aminoacylation / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Aminoacyl-tRNA synthetase, class I, anticodon-binding / Glutamate-tRNA synthetase, class I, anticodon-binding domain 1 / Glutamate-tRNA synthetase, class I, anticodon-binding domain, subdomain 1 / Arc Repressor Mutant, subunit A - #350 / Glutamate-tRNA ligase, bacterial/mitochondrial / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Glutamyl-tRNA synthetase / Anticodon binding domain / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Glutamine-tRNA ligase, alpha-bundle domain superfamily ...Aminoacyl-tRNA synthetase, class I, anticodon-binding / Glutamate-tRNA synthetase, class I, anticodon-binding domain 1 / Glutamate-tRNA synthetase, class I, anticodon-binding domain, subdomain 1 / Arc Repressor Mutant, subunit A - #350 / Glutamate-tRNA ligase, bacterial/mitochondrial / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Glutamyl-tRNA synthetase / Anticodon binding domain / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Glutamine-tRNA ligase, alpha-bundle domain superfamily / Glutamyl-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 / Glutamyl-tRNA Synthetase; Domain 3 / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / HUPs / Helicase, Ruva Protein; domain 3 / Rossmann-like alpha/beta/alpha sandwich fold / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutamate--tRNA ligase / Glutamate--tRNA ligase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKachalova, G.S. / Laurinavichiute, D. / Bartunik, H.D.
CitationJournal: To be Published
Title: Structural analysis of the non-discriminating glutamyl-tRNA synthetase from Mycobacterium tuberculosis suggests minor role of anticodon recognition in tRNA(Gln) discrimination
Authors: Laurinavichiute, D. / Bruning, M. / Shkolnaya, L.A. / Bourenkov, G.P. / Domanski, G. / Konarev, P. / Svergun, D. / Strizhov, N.I. / Kachalova, G.S. / Bartunik, H.D.
History
DepositionNov 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamyl-tRNA synthetase
B: Glutamyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)111,2072
Polymers111,2072
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glutamyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)55,6041
Polymers55,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Glutamyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)55,6041
Polymers55,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.159, 210.553, 58.145
Angle α, β, γ (deg.)90.00, 99.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutamyl-tRNA synthetase / Glutamate--tRNA ligase / GluRS


Mass: 55603.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: gltS, gltX, MT3070, MTV012.06c, Rv2992c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: P0A636, UniProt: P9WFV9*PLUS, glutamate-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200mM Ammonium Acetate, 15% (W/V)PEG4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 12, 2008 / Details: MIRROR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.69→20 Å / Num. all: 108262 / Num. obs: 98097 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.7
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 3.7 / Num. unique all: 5526 / % possible all: 94.8

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ja2

2ja2


Resolution: 1.7→10.41 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28499 5151 5 %RANDOM
Rwork0.24246 ---
all0.2446 108136 --
obs0.2446 98058 90.68 %-
Displacement parametersBiso mean: 27.326 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å2-0.39 Å2
2---0.42 Å20 Å2
3----0.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.144 Å0.148 Å
Refinement stepCycle: LAST / Resolution: 1.7→10.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7515 0 0 170 7685
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.027
X-RAY DIFFRACTIONr_angle_refined_deg2.425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.628
X-RAY DIFFRACTIONr_chiral_restr0.2
LS refinement shellResolution: 1.699→1.742 Å
RfactorNum. reflection% reflection
Rfree0.326 403 -
Rwork0.245 --
obs-7685 99.01 %

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