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- PDB-3teg: Bacterial and Eukaryotic Phenylalanyl-tRNA Synthetases Catalyze M... -

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Basic information

Entry
Database: PDB / ID: 3teg
TitleBacterial and Eukaryotic Phenylalanyl-tRNA Synthetases Catalyze Misaminoacylation of tRNAPhe with 3,4-Dihydroxy-L-Phenylalanine (L-Dopa)
ComponentsPhenylalanyl-tRNA synthetase, mitochondrial
KeywordsLIGASE / dopa / L-dopa / tRNA
Function / homology
Function and homology information


phenylalanine-tRNA ligase / Mitochondrial tRNA aminoacylation / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / tRNA processing / tRNA binding / mitochondrial matrix / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
Phenylalanyl-tRNA synthetase, class IIc, mitochondrial / Ferrodoxin-fold anticodon-binding 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 / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Bira Bifunctional Protein; Domain 2 ...Phenylalanyl-tRNA synthetase, class IIc, mitochondrial / Ferrodoxin-fold anticodon-binding 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 / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / 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) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3,4-DIHYDROXYPHENYLALANINE / Phenylalanine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2044 Å
AuthorsMoor, N. / Klipcan, L. / Safro, M.
CitationJournal: Chem.Biol. / Year: 2011
Title: Bacterial and Eukaryotic Phenylalanyl-tRNA Synthetases Catalyze Misaminoacylation of tRNA(Phe) with 3,4-Dihydroxy-L-Phenylalanine.
Authors: Moor, N. / Klipcan, L. / Safro, M.G.
History
DepositionAug 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylalanyl-tRNA synthetase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7032
Polymers48,5061
Non-polymers1971
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.185, 90.587, 96.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phenylalanyl-tRNA synthetase, mitochondrial / Phenylalanine--tRNA ligase / PheRS


Mass: 48506.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FARS1, FARS2, HSPC320 / Production host: Escherichia coli (E. coli) / References: UniProt: O95363, phenylalanine-tRNA ligase
#2: Chemical ChemComp-DAH / 3,4-DIHYDROXYPHENYLALANINE / L-DOPA


Type: L-peptide linking / Mass: 197.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO4 / Comment: neurotransmitter*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2 mM DTT, 100 mM Bis-Tris Propane,1.8 M Na-acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2009
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
ReflectionResolution: 2.2→47.853 Å / Num. all: 24066 / Num. obs: 24066 / % possible obs: 96.42 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.29 Å / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CMQ

3cmq


Resolution: 2.2044→47.853 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 21.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 1236 5.14 %random
Rwork0.1686 ---
obs0.1712 24066 96.42 %-
all-24066 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.099 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6529 Å20 Å20 Å2
2---0.2418 Å2-0 Å2
3----1.4111 Å2
Refinement stepCycle: LAST / Resolution: 2.2044→47.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 14 311 3678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073471
X-RAY DIFFRACTIONf_angle_d0.9774705
X-RAY DIFFRACTIONf_dihedral_angle_d17.791261
X-RAY DIFFRACTIONf_chiral_restr0.069493
X-RAY DIFFRACTIONf_plane_restr0.004605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2044-2.29270.28861450.22482426X-RAY DIFFRACTION95
2.2927-2.3970.25631460.20462524X-RAY DIFFRACTION98
2.397-2.52340.25521290.20052563X-RAY DIFFRACTION98
2.5234-2.68150.28191420.1942523X-RAY DIFFRACTION98
2.6815-2.88850.27711400.17752540X-RAY DIFFRACTION97
2.8885-3.17910.22391320.17042551X-RAY DIFFRACTION97
3.1791-3.6390.17611150.1412573X-RAY DIFFRACTION97
3.639-4.58420.19171510.12882520X-RAY DIFFRACTION95
4.5842-47.86410.20131360.17992610X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 1.593 Å / Origin y: 25.5924 Å / Origin z: 13.6206 Å
111213212223313233
T0.1422 Å20.0127 Å20.0223 Å2-0.1653 Å20.0146 Å2--0.1215 Å2
L0.4984 °2-0.0827 °2-0.0906 °2-1.6483 °20.1619 °2--0.5702 °2
S0.0433 Å °-0.0239 Å °0.0423 Å °-0.0093 Å °-0.0666 Å °0.0736 Å °-0.0412 Å °-0.0012 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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