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- PDB-3hfz: Crystal structure of Thermus thermophilus Phenylalanyl-tRNA synth... -

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Basic information

Entry
Database: PDB / ID: 3hfz
TitleCrystal structure of Thermus thermophilus Phenylalanyl-tRNA synthetase complexed with m-tyrosine
Components
  • Phenylalanyl-tRNA synthetase alpha chain
  • Phenylalanyl-tRNA synthetase beta chain
KeywordsLIGASE / HETERODIMER / PHENYLALANYL-TRNA / THERMUS THERMOPHILUS / TRNA / M-TYROSINE / Aminoacyl-tRNA synthetase / ATP-binding / Magnesium / Metal-binding / Nucleotide-binding / Protein biosynthesis / RNA-binding / tRNA-binding
Function / homology
Function and homology information


phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Ferrodoxin-fold anticodon-binding domain / Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain ...Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #10 / Phenylalanyl-tRNA Synthetase; Chain B, domain 3 / Phenylalanyl-trna Synthetase, Chain B, domain 3 / Ferrodoxin-fold anticodon-binding domain / Phenylalanine-tRNA ligase, class II, N-terminal / Phenylalanine-tRNA ligase alpha chain 1, bacterial / Aminoacyl tRNA synthetase class II, N-terminal domain / Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type / Phenylalanyl-tRNA synthetase, class IIc, alpha subunit / Phenylalanly tRNA synthetase, tRNA-binding-domain / tRNA synthetase, B5-domain / Phenylalanine-tRNA ligase, class IIc, beta subunit / tRNA synthetase B5 domain / B5 domain profile. / tRNA synthetase B5 domain / B3/4 domain / Ferrodoxin-fold anticodon-binding domain / Ferrodoxin-fold anticodon-binding domain superfamily / Ferredoxin-fold anticodon binding domain / Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. / Ferredoxin-fold anticodon binding domain / B3/B4 tRNA-binding domain / Phenylalanyl-tRNA synthetase-like, B3/B4 / Phenylalanyl tRNA synthetase beta chain, core domain / Phenylalanyl tRNA synthetase beta chain CLM domain / B3/4 domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Putative DNA-binding domain superfamily / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding proteins / 3-Layer(bba) Sandwich / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Plaits / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
META-TYROSINE / Phenylalanine--tRNA ligase alpha subunit / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase beta subunit / Phenylalanine--tRNA ligase alpha subunit
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsKlipcan, L. / Moor, N. / Kessler, N. / Safro, M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Eukaryotic cytosolic and mitochondrial phenylalanyl-tRNA synthetases catalyze the charging of tRNA with the meta-tyrosine
Authors: Klipcan, L. / Moor, N. / Kessler, N. / Safro, M.G.
History
DepositionMay 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 1.4Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylalanyl-tRNA synthetase alpha chain
B: Phenylalanyl-tRNA synthetase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,3924
Polymers126,0302
Non-polymers3622
Water4,342241
1
A: Phenylalanyl-tRNA synthetase alpha chain
B: Phenylalanyl-tRNA synthetase beta chain
hetero molecules

A: Phenylalanyl-tRNA synthetase alpha chain
B: Phenylalanyl-tRNA synthetase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,7848
Polymers252,0604
Non-polymers7254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area26500 Å2
ΔGint-115 kcal/mol
Surface area79590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.181, 173.181, 138.852
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-354-

HOH

21B-874-

HOH

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Components

#1: Protein Phenylalanyl-tRNA synthetase alpha chain / Phenylalanine--tRNA ligase alpha chain / PheRS


Mass: 39309.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: P27001, UniProt: Q5SGX2*PLUS, phenylalanine-tRNA ligase
#2: Protein Phenylalanyl-tRNA synthetase beta chain / Phenylalanine--tRNA ligase beta chain / PheRS


Mass: 86720.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: P27002, UniProt: Q5SGX1*PLUS, phenylalanine-tRNA ligase
#3: Chemical ChemComp-MTY / META-TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 4.77 Å3/Da / Density % sol: 74.21 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 30% (NH4)2SO4, 0.02M IMIDAZOLE-HCL, 0.001M magnesium chloride, m-tyrosine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2008
RadiationMonochromator: Aluminium or Carbon foils / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionHighest resolution: 2.899 Å / Num. all: 3671 / Num. obs: 3671 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1pys

1pys


Resolution: 2.9→47.04 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0 / SU B: 16.494 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.326 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2688 5.1 %RANDOM
Rwork0.269 ---
obs0.27 50474 99.25 %-
all-53162 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120 Å2 / Biso mean: 69.467 Å2 / Biso min: 19.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8250 0 26 241 8517
LS refinement shellResolution: 2.899→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 211 -
Rwork0.413 3671 -
all-3882 -
obs--99.51 %

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