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- PDB-5mgw: Kinetic and Structural Changes in HsmtPheRS, Induced by Pathogeni... -

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Basic information

Entry
Database: PDB / ID: 5mgw
TitleKinetic and Structural Changes in HsmtPheRS, Induced by Pathogenic Mutations in Human FARS2
ComponentsPhenylalanine--tRNA ligase, mitochondrial
KeywordsLIGASE / crystal structure of pathogenic Human mitochondrial PheRS / Molecular dynamic / kinetik study / aminoacylation
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
PHENYLALANINE / Phenylalanine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.46 Å
AuthorsKartvelishvili, E. / Tworowski, D. / Vernon, H. / Chrzanowska-Lightowlers, Z. / Moor, N. / Wang, J. / Wong, L.-J. / Safro, M.
CitationJournal: Protein Sci. / Year: 2017
Title: Kinetic and structural changes in HsmtPheRS, induced by pathogenic mutations in human FARS2.
Authors: Kartvelishvili, E. / Tworowski, D. / Vernon, H. / Moor, N. / Wang, J. / Wong, L.J. / Chrzanowska-Lightowlers, Z. / Safro, M.
History
DepositionNov 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Phenylalanine--tRNA ligase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6542
Polymers47,4891
Non-polymers1651
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.355, 90.117, 99.081
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 47488.879 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 / Phenylalanine


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


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 2 mM DTT, 100 mM bis-Tris propane pH 7 and 1.8 M sodium acetate pH 7

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.46→45.912 Å / Num. obs: 83388 / % possible obs: 100 % / Redundancy: 4.7 % / Net I/σ(I): 33.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementResolution: 1.46→45.912 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.45
RfactorNum. reflection% reflection
Rfree0.2049 2000 2.4 %
Rwork0.1851 --
obs0.1855 83373 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.51 Å2 / Biso mean: 28.2491 Å2 / Biso min: 13.36 Å2
Refinement stepCycle: final / Resolution: 1.46→45.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 12 522 3887
Biso mean--16.58 36.75 -
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063458
X-RAY DIFFRACTIONf_angle_d0.824683
X-RAY DIFFRACTIONf_chiral_restr0.077495
X-RAY DIFFRACTIONf_plane_restr0.005606
X-RAY DIFFRACTIONf_dihedral_angle_d16.1181261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.46-1.49650.34311410.317157375878100
1.4965-1.5370.3131410.289757425883100
1.537-1.58220.29081420.246857665908100
1.5822-1.63330.28241410.226757415882100
1.6333-1.69170.22781410.217357545895100
1.6917-1.75940.21891420.202757725914100
1.7594-1.83950.23441430.194858075950100
1.8395-1.93650.20451410.182957425883100
1.9365-2.05780.20561440.17358235967100
2.0578-2.21670.22981420.171658115953100
2.2167-2.43970.18971430.176758325975100
2.4397-2.79270.22021440.187258425986100
2.7927-3.51830.18681450.17695889603499
3.5183-45.93420.17981500.17366115626599

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