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- PDB-4wj4: Crystal structure of non-discriminating aspartyl-tRNA synthetase ... -

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Basic information

Entry
Database: PDB / ID: 4wj4
TitleCrystal structure of non-discriminating aspartyl-tRNA synthetase from Pseudomonas aeruginosa complexed with tRNA(Asn) and aspartic acid
Components
  • 76mer-tRNA
  • Aspartate--tRNA(Asp/Asn) ligase
KeywordsLIGASE/RNA / non-discriminating AspRS / tRNA / aminoacylation / LIGASE-RNA complex
Function / homology
Function and homology information


aspartate-tRNAAsn ligase / aspartate-tRNA(Asn) ligase activity / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / nucleic acid binding / ATP binding / cytoplasm
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
ASPARTIC ACID / : / RNA / RNA (> 10) / Aspartate--tRNA(Asp/Asn) ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.294 Å
AuthorsSuzuki, T. / Nakamura, A. / Kato, K. / Tanaka, I. / Yao, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology of Japan21370041 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis
Authors: Suzuki, T. / Nakamura, A. / Kato, K. / Soll, D. / Tanaka, I. / Sheppard, K. / Yao, M.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references / Structure summary
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate--tRNA(Asp/Asn) ligase
B: 76mer-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9163
Polymers91,7832
Non-polymers1331
Water0
1
A: Aspartate--tRNA(Asp/Asn) ligase
B: 76mer-tRNA
hetero molecules

A: Aspartate--tRNA(Asp/Asn) ligase
B: 76mer-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,8336
Polymers183,5664
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area19120 Å2
ΔGint-109 kcal/mol
Surface area65840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.913, 157.913, 146.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Aspartate--tRNA(Asp/Asn) ligase / Aspartyl-tRNA synthetase / AspRS / Non-discriminating aspartyl-tRNA synthetase / ND-AspRS


Mass: 67311.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: aspS, PA0963 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(de3) / References: UniProt: Q51422, aspartate-tRNAAsn ligase
#2: RNA chain 76mer-tRNA


Mass: 24471.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa PAO1 (bacteria) / References: GenBank: 110227054
#3: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.97 Å3/Da / Density % sol: 75.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: Trisodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.29→47.26 Å / Num. obs: 28534 / % possible obs: 99.8 % / Redundancy: 14.6 % / Net I/σ(I): 14.53

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 3.294→39.478 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 1425 5 %
Rwork0.1894 --
obs0.1912 28524 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.294→39.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4614 1622 9 0 6245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036532
X-RAY DIFFRACTIONf_angle_d0.6159202
X-RAY DIFFRACTIONf_dihedral_angle_d13.1582706
X-RAY DIFFRACTIONf_chiral_restr0.0241069
X-RAY DIFFRACTIONf_plane_restr0.003927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.294-3.41170.32221440.28652616X-RAY DIFFRACTION99
3.4117-3.54820.31971310.26562658X-RAY DIFFRACTION100
3.5482-3.70960.29921430.25112690X-RAY DIFFRACTION100
3.7096-3.9050.26951370.222673X-RAY DIFFRACTION100
3.905-4.14940.23061440.2132681X-RAY DIFFRACTION100
4.1494-4.46940.27811400.19042692X-RAY DIFFRACTION100
4.4694-4.91840.19121390.17072700X-RAY DIFFRACTION100
4.9184-5.62830.22651430.17892731X-RAY DIFFRACTION100
5.6283-7.08440.21871510.1862754X-RAY DIFFRACTION100
7.0844-39.48110.17651530.15642904X-RAY DIFFRACTION100

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