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- PDB-6wrk: Crystal structure of 3rd-generation Mj 3-nitro-tyrosine tRNA synt... -

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Basic information

Entry
Database: PDB / ID: 6wrk
TitleCrystal structure of 3rd-generation Mj 3-nitro-tyrosine tRNA synthetase ("A7") bound to 3-nitro-tyrosine
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / aminoacyl-tRNA synthetase / 3-nitro-tyrosine
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 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-type / : / Tyrosine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
META-NITRO-TYROSINE / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBeyer, J.N. / Hosseinzadeh, P. / Karplus, P.A. / Mehl, R.A. / Cooley, R.B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM114653-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM131168-02 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3F32GM120791-01S1 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Overcoming Near-Cognate Suppression in a Release Factor 1-Deficient Host with an Improved Nitro-Tyrosine tRNA Synthetase.
Authors: Beyer, J.N. / Hosseinzadeh, P. / Gottfried-Lee, I. / Van Fossen, E.M. / Zhu, P. / Bednar, R.M. / Karplus, P.A. / Mehl, R.A. / Cooley, R.B.
History
DepositionApr 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 18, 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: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8897
Polymers36,1371
Non-polymers7526
Water2,792155
1
A: Tyrosine--tRNA ligase
hetero molecules

A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,77714
Polymers72,2742
Non-polymers1,50312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area4290 Å2
ΔGint-59 kcal/mol
Surface area27850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.430, 101.430, 71.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

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Components

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


Mass: 36136.898 Da / Num. of mol.: 1 / Mutation: Y32H, H70T, D158H, I159A, L162R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: tyrS, MJ0389 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NIY / META-NITRO-TYROSINE


Type: L-peptide linking / Mass: 226.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10N2O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 22-23% PEG 300, 5% PEG 8000, 10% glycerol and 100 mM Tris pH 7.9 to 8.2
PH range: 7.9-8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2019
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→45.36 Å / Num. obs: 28169 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.998 / Net I/σ(I): 10.17
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 7238 / CC1/2: 0.31 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
Cootmodel building
PHENIXphasing
XSCALEdata scaling
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NDA

4nda


Resolution: 1.95→45.36 Å / SU ML: 0.2811 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.527
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2053 821 2.96 %
Rwork0.181 26914 -
obs0.1817 27735 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.99 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 51 155 2711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01742733
X-RAY DIFFRACTIONf_angle_d1.5643687
X-RAY DIFFRACTIONf_chiral_restr0.1002399
X-RAY DIFFRACTIONf_plane_restr0.012480
X-RAY DIFFRACTIONf_dihedral_angle_d25.58041085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.070.3781340.32294391X-RAY DIFFRACTION99.98
2.07-2.230.24721350.24424409X-RAY DIFFRACTION99.96
2.23-2.460.26711350.2024430X-RAY DIFFRACTION99.93
2.46-2.810.19421360.17694467X-RAY DIFFRACTION99.91
2.81-3.540.2181370.16084507X-RAY DIFFRACTION99.91
3.54-45.360.16521440.16084710X-RAY DIFFRACTION99.86

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