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- PDB-3akz: Crystal structure of Thermotoga maritima nondiscriminating glutam... -

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Basic information

Entry
Database: PDB / ID: 3akz
TitleCrystal structure of Thermotoga maritima nondiscriminating glutamyl-tRNA synthetase in complex with tRNAGln and a glutamyl-AMP analog
Components
  • Glutamyl-tRNA synthetase 2
  • tRNAGln
KeywordsLIGASE/RNA / Protein-rna complex / LIGASE-RNA complex
Function / homology
Function and homology information


glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytosol
Similarity search - Function
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 / Glutamyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Aminoacyl-tRNA synthetase, class I, anticodon-binding / Anticodon binding domain / : ...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 / Glutamyl-tRNA synthetase / Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily / Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2 / Aminoacyl-tRNA synthetase, class I, anticodon-binding / Anticodon binding domain / : / 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 / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / 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
O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE / RNA / RNA (> 10) / Glutamate--tRNA ligase 2
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsIto, T. / Yokoyama, S.
CitationJournal: Nature / Year: 2010
Title: Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions.
Authors: Ito, T. / Yokoyama, S.
History
DepositionJul 19, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glutamyl-tRNA synthetase 2
D: Glutamyl-tRNA synthetase 2
C: Glutamyl-tRNA synthetase 2
A: Glutamyl-tRNA synthetase 2
F: tRNAGln
H: tRNAGln
G: tRNAGln
E: tRNAGln
hetero molecules


Theoretical massNumber of molelcules
Total (without water)327,20812
Polymers325,3078
Non-polymers1,9024
Water00
1
B: Glutamyl-tRNA synthetase 2
F: tRNAGln
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8023
Polymers81,3272
Non-polymers4751
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-33 kcal/mol
Surface area30390 Å2
MethodPISA
2
D: Glutamyl-tRNA synthetase 2
H: tRNAGln
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8023
Polymers81,3272
Non-polymers4751
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-37 kcal/mol
Surface area31470 Å2
MethodPISA
3
C: Glutamyl-tRNA synthetase 2
G: tRNAGln
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8023
Polymers81,3272
Non-polymers4751
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-30 kcal/mol
Surface area31280 Å2
MethodPISA
4
A: Glutamyl-tRNA synthetase 2
E: tRNAGln
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8023
Polymers81,3272
Non-polymers4751
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-36 kcal/mol
Surface area30480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.203, 159.903, 156.166
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutamyl-tRNA synthetase 2 / Glutamate-tRNA ligase 2 / GluRS 2


Mass: 57468.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: gltX2, TM_1875 / Plasmid: PET-28B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9X2I8, glutamate-tRNA ligase
#2: RNA chain
tRNAGln


Mass: 23858.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: T7 Transcription
#3: Chemical
ChemComp-GSU / O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE


Type: L-peptide linking / Mass: 475.434 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H21N7O9S

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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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% 2-propanol, 0.2M magnesium chloride, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2009 / Details: mirrors
RadiationMonochromator: Rotated-inclined Si(111) double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.9→50 Å / Num. obs: 59965 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.109 / Net I/σ(I): 11.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 5139 / Rsym value: 0.47 / % possible all: 75.3

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AFH, 1N78

3afh

1n78


Resolution: 2.9→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0
Details: The crystal harbors twinning, and all refinement processes were performed with the twinning operator (h, -k, -l) with the twinning fraction of 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2692 -Random
Rwork0.2 ---
all-59965 --
obs-56044 81.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.772 Å20 Å2-5.637 Å2
2--19.94 Å20 Å2
3----11.168 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15420 6324 128 0 21872
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.61

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