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- PDB-7fg6: Crystal structure of the Tyrosyl-tRNA synthetase (TyrRS) in Nanoa... -

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Basic information

Entry
Database: PDB / ID: 7fg6
TitleCrystal structure of the Tyrosyl-tRNA synthetase (TyrRS) in Nanoarchaeum equitans
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / TyrRS / tRNA synthetase
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, type 4 / Tyrosine-tRNA ligase, archaeal/eukaryotic-type / : / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesNanoarchaeum equitans Kin4-M (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNoguchi, H. / Kamata, K. / Park, S.Y. / Tamura, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)17K19210 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structure of Nanoarchaeum equitans tyrosyl-tRNA synthetase and its aminoacylation activity toward tRNA Tyr with an extra guanosine residue at the 5'-terminus.
Authors: Horikoshi, T. / Noguchi, H. / Umehara, T. / Mutsuro-Aoki, H. / Kurihara, R. / Noguchi, R. / Hashimoto, T. / Watanabe, Y. / Ando, T. / Kamata, K. / Park, S.Y. / Tamura, K.
History
DepositionJul 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)43,2441
Polymers43,2441
Non-polymers00
Water19811
1
A: Tyrosine--tRNA ligase

A: Tyrosine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)86,4892
Polymers86,4892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2680 Å2
ΔGint-34 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.639, 52.639, 263.631
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Tyrosine--tRNA ligase / Tyrosyl-tRNA synthetase / TyrRS


Mass: 43244.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans Kin4-M (archaea) / Strain: Kin4-M / Gene: tyrS / Production host: Escherichia coli (E. coli) / References: UniProt: Q74MD3, tyrosine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Magnesium acetate, 0.1 M Sodium cacodylate pH6.5, 20% (w/v) PEG 8,000

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→45.59 Å / Num. obs: 11299 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 63.73 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.072 / Net I/σ(I): 14
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 10.6 % / Num. unique obs: 1606 / CC1/2: 0.69 / Rpim(I) all: 0.566 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1j1u

1j1u


Resolution: 2.8→45.59 Å / SU ML: 0.4082 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.2755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3238 481 4.28 %
Rwork0.2822 10759 -
obs0.284 11240 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.66 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 0 11 2943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592983
X-RAY DIFFRACTIONf_angle_d0.95634017
X-RAY DIFFRACTIONf_chiral_restr0.0656460
X-RAY DIFFRACTIONf_plane_restr0.0043505
X-RAY DIFFRACTIONf_dihedral_angle_d10.2032389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.20.39861430.3773478X-RAY DIFFRACTION100
3.21-4.040.38881790.29633538X-RAY DIFFRACTION100
4.04-45.590.26261590.24983743X-RAY DIFFRACTION99.87

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