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- PDB-2rd2: Glutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N... -

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Basic information

Entry
Database: PDB / ID: 2rd2
TitleGlutaminyl-tRNA synthetase mutant C229R with bound analog 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE
Components
  • Glutamine tRNA
  • Glutaminyl-tRNA synthetaseQARS
KeywordsLIGASE/RNA / protein-RNA complex / Aminoacyl-tRNA synthetase / ATP-binding / Ligase / Nucleotide-binding / Protein biosynthesis / LIGASE-RNA COMPLEX
Function / homology
Function and homology information


glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / glutamyl-tRNA aminoacylation / ATP binding / cytosol
Similarity search - Function
Glutamine-tRNA ligase, bacterial / Glutamine-tRNA synthetase / 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 / Ribosomal Protein L25; Chain P / : / tRNA synthetases class I (E and Q), anti-codon binding domain ...Glutamine-tRNA ligase, bacterial / Glutamine-tRNA synthetase / 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 / Ribosomal Protein L25; Chain P / : / 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 / Ribosomal Protein L25; Chain P / 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 / 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 / Alpha-Beta Complex / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE / RNA / RNA (> 10) / Glutamine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsBullock, T.L. / Perona, J.J.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: A rationally engineered misacylating aminoacyl-tRNA synthetase.
Authors: Bullock, T.L. / Rodriguez-Hernandez, A. / Corigliano, E.M. / Perona, J.J.
#1: Journal: RNA / Year: 2001
Title: Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization.
Authors: Sherlin, L.D. / Bullock, T.L. / Nissan, T.A. / Perona, J.J. / Lariviere, F.J. / Uhlenbeck, O.C. / Scaringe, S.A.
History
DepositionSep 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: 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 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glutamine tRNA
A: Glutaminyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7855
Polymers88,1192
Non-polymers6673
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-67 kcal/mol
Surface area31060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)237.659, 93.337, 114.826
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: RNA chain Glutamine tRNA


Mass: 24099.326 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: tRNA synthesized in vitro from a 100 nucleotide DNA template
#2: Protein Glutaminyl-tRNA synthetase / QARS / E.C.6.1.1.18 / Glutamine--tRNA ligase / GlnRS


Mass: 64019.273 Da / Num. of mol.: 1 / Mutation: C229R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: glnS / Plasmid: pQRSH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PlysS / References: UniProt: P00962, glutamine-tRNA ligase
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-QSI / 5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE


Mass: 474.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N8O8S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.65 Å3/Da / Density % sol: 66.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Sulfate11
2H2O11
3Ammonium Sulfate12
4H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorDetector: CCD / Date: Jul 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.264→119.523 Å / Num. obs: 39063 / % possible obs: 71.2 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.33-2.361.80.5821.2190410620.58247.5
2.36-2.421.80.6351.1412722710.63556.6
2.42-2.491.90.5721.2489125120.57263.9
2.49-2.572.20.4811.4586426610.48169.6
2.57-2.662.30.4161.7590526200.41670.2
2.66-2.752.30.3142.2583525620.31470.8
2.75-2.852.30.262.7570424710.2671.5
2.85-2.972.40.2263.1578124220.22672.3
2.97-3.12.40.183.9564623760.1873.8
3.1-3.252.40.1375.1542622970.13775.1
3.25-3.432.40.1136534622670.11377.2
3.43-3.642.40.0828.4523222040.08279.4
3.64-3.892.40.0758.6510420950.07579.4
3.89-4.22.50.0649482819360.06479.5
4.2-4.62.60.05411.2459117830.05478.6
4.6-5.142.60.04911.4414516010.04978.3
5.14-5.942.60.04512.6358513830.04575.6
5.94-7.272.40.04115276211290.04173.7
7.27-10.292.80.0414.925749320.0477.1
10.29-119.522.70.03121.612914790.03169.8

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
CNSphasing
RefinementResolution: 2.6→119.5 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.263 1849 4.7 %
Rwork0.209 --
obs-37292 94 %
Solvent computationBsol: 46.059 Å2
Displacement parametersBiso mean: 50.482 Å2
Baniso -1Baniso -2Baniso -3
1--10.499 Å20 Å20 Å2
2--5.808 Å20 Å2
3---4.691 Å2
Refinement stepCycle: LAST / Resolution: 2.6→119.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 1570 42 136 6032
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5qsi1.par

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