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- PDB-2ktl: Structure of C-terminal domain from mtTyrRS of A. nidulans -

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Basic information

Entry
Database: PDB / ID: 2ktl
TitleStructure of C-terminal domain from mtTyrRS of A. nidulans
ComponentsTyrosyl-tRNA synthetase
KeywordsLIGASE / S4 fold / Aminoacyl-tRNA synthetase
Function / homology
Function and homology information


tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / mitochondrion / RNA binding / ATP binding / cytosol
Similarity search - Function
Tyrosyl-tRNA synthetase, C-terminal / Tyrosyl-tRNA synthetase C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Rossmann-like alpha/beta/alpha sandwich fold / RNA-binding S4 domain superfamily
Similarity search - Domain/homology
Tyrosine--tRNA ligase / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodSOLUTION NMR / simulated annealing
AuthorsChari, N.S.
CitationJournal: To be Published
Title: Structure of C-terminal domain from mtTyrRS of A. nidulans
Authors: Hoffman, D.
History
DepositionFeb 3, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)17,6751
Polymers17,6751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Tyrosyl-tRNA synthetase


Mass: 17675.160 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ANIA_01709 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C8VNV9, UniProt: Q5BCM1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H COSY
1512D 1H-1H NOESY
1613D CBCA(CO)NH
1713D C(CO)NH
1813D HNCO
1913D HNCA
11013D HN(CA)CB
11113D (H)CCH-TOCSY
11213D 1H-15N NOESY
11313D 1H-15N TOCSY
11413D 1H-13C NOESY
11513D HN(COCA)CB
11613D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 20 mg/mL [U-100% 15N] protein, 20 mg/mL [U-100% 13C] protein, 500 mM sodium chloride, 10 mM TRIS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mg/mLentity-1[U-100% 15N]1
20 mg/mLentity-2[U-100% 13C]1
500 mMsodium chloride1
10 mMTRIS1
Sample conditionsIonic strength: 0.5 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.113Goddard, T. et al.chemical shift assignment
Sparky3.113Goddard, T. et al.data analysis
CNSBrunger, A.T. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 12

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