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- PDB-1il2: Crystal Structure of the E. coli Aspartyl-tRNA Synthetase:Yeast t... -

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Basic information

Entry
Database: PDB / ID: 1il2
TitleCrystal Structure of the E. coli Aspartyl-tRNA Synthetase:Yeast tRNAasp:aspartyl-Adenylate Complex
Components
  • ASPARTYL TRANSFER RNA
  • ASPARTYL-TRNA SYNTHETASE
KeywordsLIGASE/RNA / protein-rna complex / LIGASE-RNA COMPLEX
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / nucleic acid binding / ATP binding / cytosol
Similarity search - Function
GAD-like domain / : / : / Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) ...GAD-like domain / : / : / Aspartate-tRNA ligase, type 1 / GAD domain / GAD domain / GAD-like domain superfamily / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Gyrase A; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE / : / RNA / RNA (> 10) / Aspartate--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMoulinier, L. / Eiler, S. / Eriani, G. / Gangloff, J. / Thierry, J.C. / Gabriel, K. / McClain, W.H. / Moras, D.
CitationJournal: EMBO J. / Year: 2001
Title: The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism.
Authors: Moulinier, L. / Eiler, S. / Eriani, G. / Gangloff, J. / Thierry, J.C. / Gabriel, K. / McClain, W.H. / Moras, D.
History
DepositionMay 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: ASPARTYL TRANSFER RNA
D: ASPARTYL TRANSFER RNA
A: ASPARTYL-TRNA SYNTHETASE
B: ASPARTYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,4728
Polymers180,3554
Non-polymers1,1174
Water7,242402
1
C: ASPARTYL TRANSFER RNA
A: ASPARTYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7364
Polymers90,1782
Non-polymers5582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: ASPARTYL TRANSFER RNA
B: ASPARTYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7364
Polymers90,1782
Non-polymers5582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.800, 222.800, 80.800
Angle α, β, γ (deg.)90.00, 111.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain ASPARTYL TRANSFER RNA


Mass: 24181.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 176417
#2: Protein ASPARTYL-TRNA SYNTHETASE


Mass: 65996.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pbr322 / Production host: Escherichia coli (E. coli) / References: UniProt: P21889, aspartate-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-AMO / ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE


Mass: 462.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N6O10P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 3.51 Å3/Da / Density % sol: 64.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: ammonium sulfate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Components of the solutionsName: ammonium sulfate
Crystal grow
*PLUS
Details: Boeglin, M., (1996) Acta Crystallogr, D52, 211.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mg/mlAspRS1drop
21 mg/mltRNA1drop
31 mM1dropMgCl2
41.5 Mammonium sulfate1drop
575 mMBis-Tris-propane1drop
60.5 mMAMP-PCP1drop
71 mML-aspartic acid1drop
81.9 Mammonium sulfate1reservoir
9100 mMBis-Tris-propane1reservoir
101-3 %(v/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→11.5 Å / Redundancy: 2.3 % / Biso Wilson estimate: 45.7 Å2 / Rsym value: 3.7
Reflection
*PLUS
Num. obs: 72094 / % possible obs: 92 % / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 80 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.216

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Processing

Software
NameVersionClassification
ALMNmodel building
TSFGENmodel building
CNS1refinement
CCP4(ALMNphasing
TSFGEN)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: T. thermophilus AspRS

Resolution: 2.6→11.5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1600037.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3084 4.9 %RANDOM
Rwork0.204 ---
obs0.204 63304 84.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.14 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso mean: 46.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.06 Å20 Å24.7 Å2
2---7.6 Å20 Å2
3---2.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.6→11.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9182 3097 72 402 12753
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.211.5
X-RAY DIFFRACTIONc_mcangle_it4.82
X-RAY DIFFRACTIONc_scbond_it4.582
X-RAY DIFFRACTIONc_scangle_it6.32.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 364 4.6 %
Rwork0.318 7483 -
obs--63 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TRNA.PARAMTRNA.TOP
X-RAY DIFFRACTION3LIGAND.PARAMWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMLIGAND.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 46.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.373 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.318

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