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- PDB-4zya: The N-terminal extension domain of human asparaginyl-tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 4zya
TitleThe N-terminal extension domain of human asparaginyl-tRNA synthetase
ComponentsAsparagine--tRNA ligase, cytoplasmic
KeywordsLIGASE / asparaginyl-tRNA synthetase
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
asparaginyl-tRNA synthetase, N-terminal domain / so0334 like fold / : / 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 ...asparaginyl-tRNA synthetase, N-terminal domain / so0334 like fold / : / 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 / 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, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Asparagine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPark, J.S. / Park, M.C. / Goughnour, P. / Kim, H.S. / Kim, S.J. / Kim, H.J. / Kim, S.H. / Han, B.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Science, ICT and Future Planning of Korea2013M3A6A4043695 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
DepositionMay 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,3526
Polymers18,0932
Non-polymers2584
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-70 kcal/mol
Surface area8870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.626, 32.626, 215.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 9046.690 Da / Num. of mol.: 2 / Fragment: UNP residues 4-77
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: zinc sulfate, MES, PEG 550 MME / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 14574 / % possible obs: 97.1 % / Redundancy: 11.7 % / Rsym value: 0.107 / Net I/σ(I): 17.9
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 5.1 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→28.016 Å / Cross valid method: FREE R-VALUE / σ(F): 1.61 / Phase error: 29.18 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2541 762 5.23 %
Rwork0.2063 --
obs0.2105 14574 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→28.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 9 135 1312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011213
X-RAY DIFFRACTIONf_angle_d1.121620
X-RAY DIFFRACTIONf_dihedral_angle_d17.921477
X-RAY DIFFRACTIONf_chiral_restr0.043168
X-RAY DIFFRACTIONf_plane_restr0.004203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6551-1.78270.32721500.32832670X-RAY DIFFRACTION88
1.7827-1.96160.31411510.30632684X-RAY DIFFRACTION87
1.9616-2.24430.31651380.26062719X-RAY DIFFRACTION89
2.2443-2.82350.23191480.22722766X-RAY DIFFRACTION90
2.8235-13.66760.24081450.15452854X-RAY DIFFRACTION92

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