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- PDB-3tl4: Crystal Structure of the tRNA Binding Domain of Glutaminyl-tRNA S... -

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Basic information

Entry
Database: PDB / ID: 3tl4
TitleCrystal Structure of the tRNA Binding Domain of Glutaminyl-tRNA Synthetase from Saccharomyces cerevisiae
ComponentsGlutaminyl-tRNA synthetase
KeywordsLIGASE / glutamine / tRNA synthetase / appended domain / hinge / tRNA ligase / amidotransferase
Function / homology
Function and homology information


glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / mRNA binding / mitochondrion / ATP binding / cytosol
Similarity search - Function
Arc Repressor Mutant, subunit A - #2420 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1, domain 1 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain 2 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 1 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 / Glutamine-tRNA synthetase / : ...Arc Repressor Mutant, subunit A - #2420 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1, domain 1 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain 2 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 1 / Glutaminyl-tRNA synthetase, class Ib, non-specific RNA-binding domain, N-terminal, subdomain 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2 / Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 / Glutamine-tRNA synthetase / : / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / 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. / Helicase, Ruva Protein; domain 3 / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Glutamine--tRNA ligase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsGrant, T.D. / Snell, E.H.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural conservation of an ancient tRNA sensor in eukaryotic glutaminyl-tRNA synthetase.
Authors: Grant, T.D. / Snell, E.H. / Luft, J.R. / Quartley, E. / Corretore, S. / Wolfley, J.R. / Snell, M.E. / Hadd, A. / Perona, J.J. / Phizicky, E.M. / Grayhack, E.J.
History
DepositionAug 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Jun 13, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Glutaminyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)21,5011
Polymers21,5011
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.800, 34.620, 74.269
Angle α, β, γ (deg.)90.000, 97.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutaminyl-tRNA synthetase / Glutamine--tRNA ligase / GlnRS


Mass: 21501.047 Da / Num. of mol.: 1 / Fragment: tRNA Binding Domain (UNP residues 1-187)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GLN4, O3601, YOR168W / Plasmid: BG2483 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BCY123 / References: UniProt: P13188, glutamine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 295 K / Method: microbatch under oil / pH: 8
Details: 100mM KCl, 100mM Tris, 20% (w/v) PEG 4000, pH 8.0, microbatch under oil, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97904, 0.91162, 0.97937
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 14, 2010
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979041
20.911621
30.979371
ReflectionResolution: 2.3→73.615 Å / Num. all: 9393 / Num. obs: 9393 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rsym value: 0.1 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.426.60.491.6900213600.49100
2.42-2.576.60.3582.2851512840.358100
2.57-2.756.60.2892.7787211880.289100
2.75-2.976.60.1924761311470.192100
2.97-3.256.60.1256.1672410180.125100
3.25-3.646.60.0769.862829540.076100
3.64-4.26.50.05812.454448390.058100
4.2-5.146.40.0513.846347210.05100
5.14-7.276.30.05412.935375620.054100
7.27-26.2995.80.03319.218663200.03398.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.3→26.299 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.6 / σ(F): 1.38 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.211 448 4.77 %RANDOM
Rwork0.1822 ---
obs0.1837 9385 99.98 %-
all-9394 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.402 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 287.14 Å2 / Biso mean: 35.0726 Å2 / Biso min: 9.35 Å2
Baniso -1Baniso -2Baniso -3
1--3.6216 Å2-0 Å22.6902 Å2
2---0.8709 Å2-0 Å2
3---4.9143 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1489 0 0 82 1571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071511
X-RAY DIFFRACTIONf_angle_d1.0342033
X-RAY DIFFRACTIONf_chiral_restr0.077231
X-RAY DIFFRACTIONf_plane_restr0.004259
X-RAY DIFFRACTIONf_dihedral_angle_d14.39587
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3001-2.63270.26161420.231429363078
2.6327-3.31590.28371420.194929723114
3.3159-26.30110.17021640.160630293193

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