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- PDB-5xix: The canonical domain of human asparaginyl-tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 5xix
TitleThe canonical domain of human asparaginyl-tRNA synthetase
ComponentsAsparagine--tRNA ligase, cytoplasmic
KeywordsLIGASE
Function / homology
Function and homology information


asparagine-tRNA ligase / asparagine-tRNA ligase activity / asparaginyl-tRNA aminoacylation / CCR3 chemokine receptor binding / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / cerebral cortex development / cell migration / nucleic acid binding / protein dimerization activity ...asparagine-tRNA ligase / asparagine-tRNA ligase activity / asparaginyl-tRNA aminoacylation / CCR3 chemokine receptor binding / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / cerebral cortex development / cell migration / nucleic acid binding / protein dimerization activity / extracellular exosome / ATP binding / cytosol / cytoplasm
Similarity search - Function
: / Asparaginal-tRNA synthetase, N-terminal domain / Asparagine-tRNA ligase / 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 ...: / Asparaginal-tRNA synthetase, N-terminal domain / Asparagine-tRNA ligase / 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. / 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
Asparagine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPark, J.S. / Han, B.W.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research FoundationNRF-2013M-3A6A-4043695 Korea, Republic Of
National Research Foundation2011-0030001 Korea, Republic Of
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Unique N-terminal extension domain of human asparaginyl-tRNA synthetase elicits CCR3-mediated chemokine activity.
Authors: Park, J.S. / Park, M.C. / Lee, K.Y. / Goughnour, P.C. / Jeong, S.J. / Kim, H.S. / Kim, H.J. / Lee, B.J. / Kim, S. / Han, B.W.
History
DepositionApr 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Asparagine--tRNA ligase, cytoplasmic
B: Asparagine--tRNA ligase, cytoplasmic
C: Asparagine--tRNA ligase, cytoplasmic
D: Asparagine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,51731
Polymers216,0304
Non-polymers2,48727
Water19,9251106
1
A: Asparagine--tRNA ligase, cytoplasmic
D: Asparagine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,12014
Polymers108,0152
Non-polymers1,10512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-53 kcal/mol
Surface area35550 Å2
MethodPISA
2
B: Asparagine--tRNA ligase, cytoplasmic
C: Asparagine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,39617
Polymers108,0152
Non-polymers1,38115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11140 Å2
ΔGint-54 kcal/mol
Surface area34890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.350, 127.103, 163.475
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Asparagine--tRNA ligase, cytoplasmic / Asparaginyl-tRNA synthetase / AsnRS


Mass: 54007.523 Da / Num. of mol.: 4 / Fragment: UNP residues 98-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NARS / Production host: Escherichia coli (E. coli) / References: UniProt: O43776, asparagine-tRNA ligase
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1106 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: glycerol, potassium phosphate, PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 112318 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 19.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XGT

2xgt


Resolution: 2.25→29.617 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.51
RfactorNum. reflection% reflection
Rfree0.2287 5527 4.93 %
Rwork0.1767 --
obs0.1793 112162 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→29.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13690 0 162 1106 14958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814153
X-RAY DIFFRACTIONf_angle_d1.10119108
X-RAY DIFFRACTIONf_dihedral_angle_d14.7165316
X-RAY DIFFRACTIONf_chiral_restr0.042032
X-RAY DIFFRACTIONf_plane_restr0.0052471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.27560.27171900.20493566X-RAY DIFFRACTION100
2.2756-2.30230.24361800.20863499X-RAY DIFFRACTION100
2.3023-2.33040.26782020.20543482X-RAY DIFFRACTION100
2.3304-2.35990.29252020.20593515X-RAY DIFFRACTION100
2.3599-2.39090.26041790.19833482X-RAY DIFFRACTION100
2.3909-2.42370.28191990.20243489X-RAY DIFFRACTION100
2.4237-2.45830.27991970.19843553X-RAY DIFFRACTION100
2.4583-2.49490.27141830.19783480X-RAY DIFFRACTION100
2.4949-2.53390.24141670.2013541X-RAY DIFFRACTION100
2.5339-2.57540.31551960.19693517X-RAY DIFFRACTION100
2.5754-2.61980.25911900.19373544X-RAY DIFFRACTION100
2.6198-2.66740.2341960.18653477X-RAY DIFFRACTION100
2.6674-2.71870.23141740.18423541X-RAY DIFFRACTION100
2.7187-2.77410.2631680.18373556X-RAY DIFFRACTION100
2.7741-2.83440.27381700.19383560X-RAY DIFFRACTION100
2.8344-2.90030.25831860.19753521X-RAY DIFFRACTION100
2.9003-2.97280.25271680.19543549X-RAY DIFFRACTION100
2.9728-3.05310.23141900.18993541X-RAY DIFFRACTION100
3.0531-3.14280.26421810.18363550X-RAY DIFFRACTION100
3.1428-3.24410.22411760.18263551X-RAY DIFFRACTION100
3.2441-3.35990.2191750.18153545X-RAY DIFFRACTION100
3.3599-3.49420.24561660.18473598X-RAY DIFFRACTION100
3.4942-3.6530.22111830.17553569X-RAY DIFFRACTION100
3.653-3.84520.22361810.173571X-RAY DIFFRACTION100
3.8452-4.08560.24551890.16213585X-RAY DIFFRACTION100
4.0856-4.40010.15461920.14343577X-RAY DIFFRACTION100
4.4001-4.84110.18581880.13643603X-RAY DIFFRACTION100
4.8411-5.53770.20381870.15053632X-RAY DIFFRACTION100
5.5377-6.96190.22541830.18473667X-RAY DIFFRACTION100
6.9619-29.61910.1721890.16643774X-RAY DIFFRACTION99

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