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- PDB-4hjx: Crystal structure of F2YRS complexed with F2Y -

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Basic information

Entry
Database: PDB / ID: 4hjx
TitleCrystal structure of F2YRS complexed with F2Y
ComponentsTyrosine-tRNA ligaseTyrosine—tRNA ligase
KeywordsLIGASE / AMINOACYL-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 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / 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. / HUPs ...Tyrosine-tRNA ligase, type 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / 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. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3,5-difluoro-L-tyrosine / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanococcus Jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsWang, J. / Tian, C. / Gong, W. / Li, F. / Shi, P. / Li, J. / Ding, W.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: A genetically encoded 19F NMR probe for tyrosine phosphorylation.
Authors: Li, F. / Shi, P. / Li, J. / Yang, F. / Wang, T. / Zhang, W. / Gao, F. / Ding, W. / Li, D. / Li, J. / Xiong, Y. / Sun, J. / Gong, W. / Tian, C. / Wang, J.
History
DepositionOct 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-tRNA ligase
B: Tyrosine-tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5384
Polymers72,1042
Non-polymers4342
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-27 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.307, 101.307, 71.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 36051.777 Da / Num. of mol.: 2 / Mutation: Y32R,L65Y,H70G,F108N,Q109C,D158N,L162S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus Jannaschii DSM 2661 (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: tyrS, MJ0389 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57834
#2: Chemical ChemComp-F2Y / 3,5-difluoro-L-tyrosine


Type: L-peptide linking / Mass: 217.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9F2NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.55 Å3/Da / Density % sol: 51.84 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: Rigaku Satun 944 HG / Detector: CCD / Date: Aug 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.91→50 Å / Num. all: 16153 / Num. obs: 16105 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 17.5
Reflection shellResolution: 2.91→3.01 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1601 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREP- auto MRphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J1U

1j1u


Resolution: 2.91→24.594 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 804 5 %RANDOM
Rwork0.2113 ---
all0.2141 16153 --
obs0.2135 16069 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.91→24.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4883 0 30 64 4977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024993
X-RAY DIFFRACTIONf_angle_d0.5676706
X-RAY DIFFRACTIONf_dihedral_angle_d12.0161962
X-RAY DIFFRACTIONf_chiral_restr0.038738
X-RAY DIFFRACTIONf_plane_restr0.002863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9102-3.09220.39071370.27262525X-RAY DIFFRACTION100
3.0922-3.33040.30331270.24832517X-RAY DIFFRACTION100
3.3304-3.66450.31811520.21182509X-RAY DIFFRACTION100
3.6645-4.19250.23421230.18092564X-RAY DIFFRACTION100
4.1925-5.27360.23841290.18482548X-RAY DIFFRACTION100
5.2736-24.59470.23861360.22812602X-RAY DIFFRACTION100

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