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- PDB-6wn2: Tyrosyl t-RNA Synthetase Mutant from E.coli Complexed with sulfot... -

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Basic information

Entry
Database: PDB / ID: 6wn2
TitleTyrosyl t-RNA Synthetase Mutant from E.coli Complexed with sulfotyrosine
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / TyrRS / sulfotyrosine
Function / homology
Function and homology information


tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / protein homodimerization activity / RNA binding / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine-tRNA ligase, bacterial-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 / S4 RNA-binding domain / RNA-binding S4 domain ...Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine-tRNA ligase, bacterial-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 / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / S4 RNA-binding domain profile.
Similarity search - Domain/homology
O-SULFO-L-TYROSINE / Tyrosine--tRNA ligase / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.78 Å
AuthorsBeltran, D.G. / Zhang, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CLP 1846908 United States
CitationJournal: Nat Commun / Year: 2020
Title: Functional genetic encoding of sulfotyrosine in mammalian cells.
Authors: He, X. / Chen, Y. / Beltran, D.G. / Kelly, M. / Ma, B. / Lawrie, J. / Wang, F. / Dodds, E. / Zhang, L. / Guo, J. / Niu, W.
History
DepositionApr 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,18320
Polymers71,9252
Non-polymers2,25818
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-134 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.093, 93.904, 99.900
Angle α, β, γ (deg.)90.000, 92.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35962.676 Da / Num. of mol.: 2 / Mutation: L71V, W129F,D182G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tyrS, CR539_12835 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3Q0MY83, UniProt: P0AGJ9*PLUS, tyrosine-tRNA ligase

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Non-polymers , 5 types, 376 molecules

#2: Chemical ChemComp-TYS / O-SULFO-L-TYROSINE


Type: L-peptide linking / Mass: 261.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 288 K / Method: vapor diffusion
Details: 0.1 M Hepes pH 7.5, 2.2 M ammonium sulfate and 2.5-3% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97928 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.78→99.795 Å / Num. all: 66097 / Num. obs: 66097 / % possible obs: 98.4 % / Redundancy: 6.7 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Rsym value: 0.073 / Net I/av σ(I): 7.8 / Net I/σ(I): 14.1 / Num. measured all: 443386
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.78-1.886.51.7980.46207294920.7531.9531.7981.197.2
1.88-1.996.80.8340.96239591490.3420.9030.8342.498.5
1.99-2.136.90.4391.75919386050.180.4750.4394.599
2.13-2.36.80.2572.95409379550.1060.2780.2577.498.7
2.3-2.526.70.1584.74935173340.0650.1710.1581197.7
2.52-2.8170.0987.64699266900.040.1050.09817.199.4
2.81-3.256.60.06311.43934659270.0260.0680.0632599.4
3.25-3.986.20.04116.23046449170.0170.0440.04137.397.6
3.98-5.636.60.03318.82576539050.0140.0360.03345.799.2
5.63-36.1126.50.03217.91371521230.0130.0340.03246.397

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: MIR / Resolution: 1.78→36.14 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.596 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.121
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 3406 5.2 %RANDOM
Rwork0.1824 ---
obs0.1845 62565 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 122.46 Å2 / Biso mean: 35.448 Å2 / Biso min: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20.03 Å2
2---1.43 Å2-0 Å2
3---0.75 Å2
Refinement stepCycle: final / Resolution: 1.78→36.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 0 138 368 5528
Biso mean--53.14 43.56 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135260
X-RAY DIFFRACTIONr_bond_other_d00.0174825
X-RAY DIFFRACTIONr_angle_refined_deg1.41.647091
X-RAY DIFFRACTIONr_angle_other_deg1.3491.57811211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28723.403288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34815880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1011528
X-RAY DIFFRACTIONr_chiral_restr0.0710.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021106
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 240 -
Rwork0.324 4613 -
all-4853 -
obs--97.82 %

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