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

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Basic information

Entry
Database: PDB / ID: 5mgv
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--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 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 24, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4May 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

Downloads & links

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Assembly

Deposited unit
A: Phenylalanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)47,5201
Polymers47,5201
Non-polymers00
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.770, 90.370, 95.170
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: 47519.938 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 50.37 %
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: 2.05→50.05 Å / Num. obs: 28291 / % possible obs: 100 % / Redundancy: 19.8 % / Net I/σ(I): 25.22

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Processing

Software
NameVersionClassification
CNSrefinement
PDB_EXTRACT3.2data extraction
RefinementResolution: 2.05→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2711 1373 4.5 %
Rwork0.2275 --
obs-28291 93.2 %
Solvent computationBsol: 41.2549 Å2
Displacement parametersBiso max: 118.37 Å2 / Biso mean: 31.0362 Å2 / Biso min: 10.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.336 Å20 Å20 Å2
2---1.165 Å20 Å2
3----1.172 Å2
Refinement stepCycle: final / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 249 0 3607
Biso mean--42.42 --
Num. residues----405
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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