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- PDB-8p8x: Crystal structure of a pathogenic mutant variant of human mitocho... -

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Basic information

Entry
Database: PDB / ID: 8p8x
TitleCrystal structure of a pathogenic mutant variant of human mitochodnrial PheRS
ComponentsPhenylalanine--tRNA ligase, mitochondrial
KeywordsLIGASE / Phenylalanyl-tRNA synthetase / FARS2 / mitochondria / mitochondrial disease / class II aminoacyl-tRNA ligase / alpha-beta domain / ATP binding / amino acid binding
Function / homology
Function and homology information


phenylalanine-tRNA ligase / Mitochondrial tRNA aminoacylation / phenylalanyl-tRNA aminoacylation / phenylalanine-tRNA ligase activity / 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 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) / 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)
Similarity search - Domain/homology
PHENYLALANINE / Phenylalanine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsChen, W. / Kuhle, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol.Genet.Metab. / Year: 2023
Title: Clinical and molecular characterization of novel FARS2 variants causing neonatal mitochondrial disease.
Authors: Chen, W. / Rehsi, P. / Thompson, K. / Yeo, M. / Stals, K. / He, L. / Schimmel, P. / Chrzanowska-Lightowlers, Z.M.A. / Wakeling, E. / Taylor, R.W. / Kuhle, B.
History
DepositionJun 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylalanine--tRNA ligase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5792
Polymers48,4141
Non-polymers1651
Water8,593477
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18970 Å2
Unit cell
Length a, b, c (Å)54.529, 88.460, 97.381
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 Phenylalanine--tRNA ligase, mitochondrial / Phenylalanyl-tRNA synthetase / PheRS


Mass: 48413.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FARS2, FARS1, HSPC320 / Production host: Escherichia coli (E. coli) / References: UniProt: O95363, phenylalanine-tRNA ligase
#2: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.7 M sodium acetate trihydrate pH 7, 0.1 M BIS-TRIS propane pH 7, 0.1 M MgCl2, 1% v/v 1,2-Butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.46→36.32 Å / Num. obs: 82262 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.016 / Rrim(I) all: 0.042 / Χ2: 0.95 / Net I/σ(I): 21 / Num. measured all: 546378
Reflection shellResolution: 1.46→1.48 Å / % possible obs: 95.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.631 / Num. measured all: 17715 / Num. unique obs: 3860 / CC1/2: 0.792 / Rpim(I) all: 0.323 / Rrim(I) all: 0.713 / Χ2: 0.9 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→36.32 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1668 2000 2.43 %
Rwork0.1455 --
obs0.1461 82178 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→36.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 12 477 3832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173480
X-RAY DIFFRACTIONf_angle_d1.8954713
X-RAY DIFFRACTIONf_dihedral_angle_d11.159449
X-RAY DIFFRACTIONf_chiral_restr0.308498
X-RAY DIFFRACTIONf_plane_restr0.015610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.50.25621360.20515428X-RAY DIFFRACTION96
1.5-1.540.17561400.1595655X-RAY DIFFRACTION100
1.54-1.580.19811430.13825710X-RAY DIFFRACTION100
1.58-1.630.18091410.13055660X-RAY DIFFRACTION100
1.63-1.690.17361420.12815691X-RAY DIFFRACTION100
1.69-1.760.17611430.12585727X-RAY DIFFRACTION100
1.76-1.840.17841410.12935669X-RAY DIFFRACTION100
1.84-1.940.17461420.1295705X-RAY DIFFRACTION100
1.94-2.060.17541440.13025740X-RAY DIFFRACTION100
2.06-2.220.16161430.13545740X-RAY DIFFRACTION100
2.22-2.440.17241440.14065766X-RAY DIFFRACTION100
2.44-2.790.18041440.15635780X-RAY DIFFRACTION100
2.79-3.520.17261450.15275826X-RAY DIFFRACTION100
3.52-36.320.14071520.15146081X-RAY DIFFRACTION100

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