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- PDB-1c0a: CRYSTAL STRUCTURE OF THE E. COLI ASPARTYL-TRNA SYNTHETASE : TRNAA... -

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Basic information

Entry
Database: PDB / ID: 1c0a
TitleCRYSTAL STRUCTURE OF THE E. COLI ASPARTYL-TRNA SYNTHETASE : TRNAASP : ASPARTYL-ADENYLATE COMPLEX
Components
  • ASPARTYL TRNA
  • 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 / ADENOSINE MONOPHOSPHATE / : / RNA / RNA (> 10) / Aspartate--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsEiler, S. / Dock-Bregeon, A.-C. / Moulinier, L. / Thierry, J.-C. / Moras, D.
CitationJournal: EMBO J. / Year: 1999
Title: Synthesis of aspartyl-tRNA(Asp) in Escherichia coli--a snapshot of the second step.
Authors: Eiler, S. / Dock-Bregeon, A. / Moulinier, L. / Thierry, J.C. / Moras, D.
History
DepositionJul 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: ASPARTYL TRNA
A: ASPARTYL TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3395
Polymers90,4342
Non-polymers9063
Water9,260514
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.200, 101.200, 231.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

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RNA chain / Protein , 2 types, 2 molecules BA

#1: RNA chain ASPARTYL TRNA


Mass: 24995.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTRC99 / Production host: Escherichia coli (E. coli) / References: GenBank: ECOTRD1
#2: Protein ASPARTYL TRNA SYNTHETASE / E.C.6.1.1.12 / ASPARTATE-TRNA LIGASE / ASPRS


Mass: 65438.734 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 517 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-AMO / ASPARTYL-ADENOSINE-5'-MONOPHOSPHATE


Mass: 462.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N6O10P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 3.28 Å3/Da / Density % sol: 62.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: AMMONIUM SULFATE, GLYCEROL, BIS-TRIS-PROPANE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2GLYCEROL11
3BIS-TRIS-PROPANE11
4(NH4)2SO412
5GLYCEROL12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1drop
34.7 mg/mltRNAAsp1drop
42 mM1dropMgCl2
50.25 mMEDTA1drop
65 mMsodium cacodylate1drop
715 %glycerol1reservoir
82 Mammonium sulfate1reservoir
950 mMBis-Tris-propane-HCl1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.3675
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3675 Å / Relative weight: 1
ReflectionResolution: 2.4→12 Å / Num. obs: 46618 / % possible obs: 98.1 % / Redundancy: 5.6 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 93.2 % / Rmerge(I) obs: 0.214

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementResolution: 2.4→12 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2763619.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3536 7.6 %RANDOM
Rwork0.208 ---
obs0.208 46618 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.19 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20 Å20 Å2
2---1.91 Å20 Å2
3---3.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 1655 59 514 6820
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.51
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 580 7.8 %
Rwork0.248 6856 -
obs--95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA-SE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION4LIGAND.PARAMLIGAND.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 43082
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.324
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.73
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.51

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