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- PDB-1qtq: GLUTAMINYL-TRNA SYNTHETASE COMPLEXED WITH TRNA AND AN AMINO ACID ... -

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Basic information

Entry
Database: PDB / ID: 1qtq
TitleGLUTAMINYL-TRNA SYNTHETASE COMPLEXED WITH TRNA AND AN AMINO ACID ANALOG
Components
  • PROTEIN (GLUTAMINYL-TRNA SYNTHETASE)
  • RNA (TRNA GLN II )
KeywordsLIGASE/RNA / TRNA SYNTHETASE / GLUTAMINE / TRNAGLN / E. COLI / COMPLEX / 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 / Glutamyl/glutaminyl-tRNA synthetase, class Ib, 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 / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / tRNA synthetases class I (E and Q), 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 / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRath, V.L. / Silvian, L.F. / Beijer, B. / Sproat, B.S. / Steitz, T.A.
CitationJournal: Structure / Year: 1998
Title: How glutaminyl-tRNA synthetase selects glutamine.
Authors: Rath, V.L. / Silvian, L.F. / Beijer, B. / Sproat, B.S. / Steitz, T.A.
History
DepositionJan 28, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: 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: RNA (TRNA GLN II )
A: PROTEIN (GLUTAMINYL-TRNA SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3547
Polymers87,4952
Non-polymers8595
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)238.780, 93.360, 115.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: RNA chain RNA (TRNA GLN II )


Mass: 24060.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Protein PROTEIN (GLUTAMINYL-TRNA SYNTHETASE) / GLNRS


Mass: 63434.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00962, glutamine-tRNA ligase
#3: Chemical
ChemComp-SO4 / SULFATE ION / QSI


Mass: 96.063 Da / Num. of mol.: 4 / 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


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.67 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M AMMONIUM SULFATE, 20 MM MGSO4, 80 MM PIPES, PH 7.0, 1 MM QSI, AND 1:1 MOLAR RATIO OF TRNA TO PROTEIN AT 17 DEGREES C BY THE HANGING DROP METHOD., vapor diffusion - hanging drop, temperature 290.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1AMMONIUM SULFATE11
2MGSO411
3PIPES11
4AMMONIUM SULFATE12
5MGSO412
6PIPES12
7AMMONIUM SULFATE13
8MGSO413
9GLYCEROL13
10PIPES13
11SODIUM AZIDE13
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
Temperature: 17 ℃ / PH range low: 7.2 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
280 mMPIPES1reservoir
320 mM1reservoirMgCl2
420 mMbeta-mercaptoethanol1reservoir
51 mMQSI1reservoir
1tRNA enzyme1drop
61
71
81
91
101
111

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995 / Details: PT COATED SI MIRROR
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.25→28 Å / Num. obs: 51376 / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.084
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 1 % / Rmerge(I) obs: 0.534 / % possible all: 67.7
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 28 Å / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 34.5 Å2
Reflection shell
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 2.3 Å / % possible obs: 67.7 % / Redundancy: 1 % / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GTR

1gtr


Resolution: 2.25→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1087461.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED RESIDUES 1 - 7, 443 - 453, AND 548 - 553 OF THE PROTEIN AND NUCLEOTIDE 901 OF THE TRNA ARE DISORDERED IN THE CRYSTAL STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 5205 10.1 %RANDOM
Rwork0.244 ---
obs0.244 51376 83.6 %-
Displacement parametersBiso mean: 49.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.57 Å20 Å20 Å2
2--1.46 Å20 Å2
3---4.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.45 Å
Luzzati d res low-30 Å
Luzzati sigma a0.46 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 1570 52 160 6063
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.23
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.461.5
X-RAY DIFFRACTIONx_mcangle_it5.072
X-RAY DIFFRACTIONx_scbond_it4.952
X-RAY DIFFRACTIONx_scangle_it6.72.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.472 692 10 %
Rwork0.461 6203 -
obs--68 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOP.SO4
X-RAY DIFFRACTION2PARAM.SO4TOP_NDBX3.DNA
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION4QSI.PARTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23
LS refinement shell
*PLUS
Rfactor obs: 0.461

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