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- PDB-3tup: Crystal structure of human mitochondrial PheRS complexed with tRN... -

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Basic information

Entry
Database: PDB / ID: 3tup
TitleCrystal structure of human mitochondrial PheRS complexed with tRNAPhe in the active open state
Components
  • Phenylalanyl-tRNA synthetase, mitochondrial
  • Thermus thermophilus tRNAPhe
KeywordsLIGASE/RNA / class II aaRS / RRM fold / aminoacylation / mitochondria / LIGASE-RNA complex
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
RNA / RNA (> 10) / Phenylalanine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsSafro, M. / Klipcan, L. / Moor, N. / Finarov, I. / Kessler, N. / Sukhanova, M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal Structure of Human Mitochondrial PheRS Complexed with tRNA(Phe) in the Active "Open" State.
Authors: Klipcan, L. / Moor, N. / Finarov, I. / Kessler, N. / Sukhanova, M. / Safro, M.G.
History
DepositionSep 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Feb 1, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylalanyl-tRNA synthetase, mitochondrial
T: Thermus thermophilus tRNAPhe


Theoretical massNumber of molelcules
Total (without water)72,9932
Polymers72,9932
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-16 kcal/mol
Surface area31100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.041, 116.041, 123.276
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 48506.043 Da / Num. of mol.: 1 / Fragment: mitochondrial PheRS, UNP residues 38-451
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: RNA chain Thermus thermophilus tRNAPhe


Mass: 24486.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Thermus (bacteria)

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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: 3.28 Å3/Da / Density % sol: 62.53 %
Crystal growTemperature: 292 K / Method: small tubes / pH: 7
Details: 0.2 M ammonium sulfate, 100 mM MES mono-hydrate, pH 7, and 30 % w/v PEG-MME 5,000, SMALL TUBES, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 3.05→38.95 Å / Num. all: 18827 / Num. obs: 18827 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.05-3.411100
3.41-3.671100
3.67-4.041100
4.04-4.621100
4.62-5.821100
5.82-38.94197

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Processing

Software
NameClassification
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→38.94 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2951 811 random
Rwork0.245 --
all0.2452 18615 -
obs0.245 18615 -
Refinement stepCycle: LAST / Resolution: 3.05→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 1581 0 0 4928
Refine LS restraintsType: f_angle_d / Dev ideal: 1.54

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