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- PDB-1o0c: CRYSTAL STRUCTURE OF L-GLUTAMATE AND AMPCPP BOUND TO GLUTAMINE AM... -

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Basic information

Entry
Database: PDB / ID: 1o0c
TitleCRYSTAL STRUCTURE OF L-GLUTAMATE AND AMPCPP BOUND TO GLUTAMINE AMINOACYL TRNA SYNTHETASE
Components
  • Glutaminyl tRNA
  • Glutaminyl-tRNA synthetase
KeywordsLIGASE/RNA / ENGINEERED TRNA / TRNA-PROTEIN COMPLEX / amino acid specificity / 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
ADENOSINE MONOPHOSPHATE / GLUTAMIC ACID / : / RNA / RNA (> 10) / Glutamine--tRNA ligase / Glutamine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsBullock, T.L. / Perona, J.J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Amino Acid Discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants
Authors: Bullock, T.L. / Uter, N. / Nissan, T.A. / Perona, J.J.
History
DepositionFeb 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 21, 2015Group: Refinement description
Revision 1.4Oct 27, 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 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,3136
Polymers87,6262
Non-polymers6864
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)241.1, 94.58, 116.08
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

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RNA chain / Protein , 2 types, 2 molecules BA

#1: RNA chain Glutaminyl tRNA / TRNA(GLN) / transfer RNA-Gln II


Mass: 24060.287 Da / Num. of mol.: 1 / Mutation: U1G to facilitate in vitro transcription / Source method: obtained synthetically
Details: PRODUCT OF RUNOFF T7 POLYMERASE TRANSCRIPTION FROM A DOUBLE HELICAL DNA TEMPLATE
References: EMBL: 43058
#2: Protein Glutaminyl-tRNA synthetase / E.C.6.1.1.18 / Glutamine--tRNA ligase / glutamine tRNA synthetase / GlnRS /


Mass: 63565.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: complexed with AMPCPP, see REMARK 600 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GLNS / Plasmid: pSJW1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21-DE3 (PlysS)
References: UniProt: P00962, UniProt: A0A140NAB7*PLUS, glutamine-tRNA ligase

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Non-polymers , 4 types, 148 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.77 Å3/Da / Density % sol: 67.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium Sulfate, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2(NH4)2SO412
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 Mammonium sulfate1reservoir
220 mMPIPES1reservoirpH7.0
310 mM1reservoirMgSO4
420 mMbeta-mercaptoethanol1reservoir
52.25 Mammonium sulfate1drop
620 mMPIPES1droppH7.0
710 mM1dropMgSO4
820 mMbeta-mercaptoethanol1drop
960 mMglutamine1drop
105 mg/mlprotein1drop
112 mMAMPCPP1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1 Å
DetectorType: UCSD MARK II / Detector: AREA DETECTOR / Date: Jun 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→41 Å / Num. all: 46224 / Num. obs: 45855 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 55.4 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.06 / Net I/σ(I): 8.9
Reflection shellResolution: 2.5→2.8 Å / Rmerge(I) obs: 0.529 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 41.2 Å / Num. measured all: 159330 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 99.2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLOR98refinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2292 5 %RANDOM
Rwork0.213 ---
all0.215 45855 --
obs0.215 45855 --
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4279 1570 43 144 6036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.54
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS

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