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- PDB-1n3l: Crystal structure of a human aminoacyl-tRNA synthetase cytokine -

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Basic information

Entry
Database: PDB / ID: 1n3l
TitleCrystal structure of a human aminoacyl-tRNA synthetase cytokine
Componentstyrosyl-tRNA synthetase
KeywordsLIGASE / Rossmann fold as catalytic domain / unique anticodon recognition domain / dimer
Function / homology
Function and homology information


interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process ...interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process / extracellular space / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...Tyrosine-tRNA ligase / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Nucleic acid-binding, OB-fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tyrosine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.18 Å
AuthorsYang, X.-L. / Skene, R.J. / McRee, D.E. / Schimmel, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal structure of a human aminoacyl-tRNA synthetase cytokine
Authors: Yang, X.-L. / Skene, R.J. / McRee, D.E. / Schimmel, P.
History
DepositionOct 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7027
Polymers42,1341
Non-polymers5686
Water5,693316
1
A: tyrosyl-tRNA synthetase
hetero molecules

A: tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,40414
Polymers84,2672
Non-polymers1,13712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area5010 Å2
ΔGint-120 kcal/mol
Surface area30570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.595, 162.392, 35.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2154-

HOH

21A-2242-

HOH

DetailsThe other monomer of the dimer is generated by the two fold axis: -x, -y, z

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Components

#1: Protein tyrosyl-tRNA synthetase


Mass: 42133.559 Da / Num. of mol.: 1 / Fragment: mini TyrRS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P54577, tyrosine-tRNA ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.58 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.38
Details: (NH4)2SO4, NaH2PO4, K2HPO4, acetone, pH 6.38, VAPOR DIFFUSION, SITTING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 31, 2002 / Details: flat mirror (vertical focusing)
RadiationMonochromator: single crystal Si(111) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.18→30 Å / Num. all: 134129 / Num. obs: 134129 / % possible obs: 92.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 55.2
Reflection shellResolution: 1.18→1.22 Å / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.004 / Num. unique all: 8418 / Rsym value: 0.699 / % possible all: 59
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 93 %
Reflection shell
*PLUS
% possible obs: 59 % / Mean I/σ(I) obs: 1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
SHELXL-97refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.18→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2228 6310 random
Rwork0.1797 --
all0.1802 124326 -
obs0.1802 124326 -
Refinement stepCycle: LAST / Resolution: 1.18→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 32 316 2981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.032
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2159 / Rfactor Rwork: 0.1737
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.5

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