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- PDB-6wrq: Crystal structure of Mj 3-nitro-tyrosine tRNA synthetase (5B) S15... -

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Basic information

Entry
Database: PDB / ID: 6wrq
TitleCrystal structure of Mj 3-nitro-tyrosine tRNA synthetase (5B) S158C variant 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: 1.85 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 / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
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)36,7636
Polymers36,1041
Non-polymers6605
Water3,801211
1
A: Tyrosine--tRNA ligase
hetero molecules

A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,52712
Polymers72,2082
Non-polymers1,31910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area4040 Å2
ΔGint-58 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.000, 102.000, 71.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
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-551-

HOH

21A-598-

HOH

31A-711-

HOH

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Components

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


Mass: 36103.934 Da / Num. of mol.: 1 / Mutation: Y32H, H70C, D158C, 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / 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 / Nitrotyrosine


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 / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 22-23% PEG 300, 5% PEG 8000, 10% glycerol and 100 mM Tris pH 7.9-8.2
PH range: 7.9-8.2

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Si / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2018
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.85→45.62 Å / Num. obs: 33358 / % possible obs: 100 % / Redundancy: 15.3 % / CC1/2: 0.99 / Net I/σ(I): 15.7
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 0.89 / Num. unique obs: 9042 / CC1/2: 0.434 / % possible all: 100

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.17.1_3660refinement
PHENIXphasing
XSCALEdata scaling
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NDA

4nda


Resolution: 1.85→45.62 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 1227 3.74 %
Rwork0.1818 31597 -
obs0.1827 32824 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.87 Å2 / Biso mean: 44.1054 Å2 / Biso min: 20.27 Å2
Refinement stepCycle: final / Resolution: 1.85→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 75 211 2776
Biso mean--64.94 47.63 -
Num. residues----310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.920.42241340.391434463580
1.92-2.010.32891350.290234553590
2.01-2.120.2821340.232834653599
2.12-2.250.231330.206334433576
2.25-2.420.20811350.182534713606
2.42-2.670.19461360.169535063642
2.67-3.050.21481370.167735133650
3.05-3.850.18641380.155635563694
3.85-45.620.17631450.167537423887

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