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- PDB-2mx1: Structure of the E. coli Threonylcarbamoyl-AMP Synthase TSAC -

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Basic information

Entry
Database: PDB / ID: 2mx1
TitleStructure of the E. coli Threonylcarbamoyl-AMP Synthase TSAC
ComponentsThreonylcarbamoyl-AMP synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


L-threonylcarbamoyladenylate synthase / L-threonylcarbamoyladenylate synthase / tRNA threonylcarbamoyladenosine modification / regulation of translational fidelity / nucleotidyltransferase activity / rRNA processing / double-stranded RNA binding / tRNA binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Threonylcarbamoyl-AMP synthase / Threonylcarbamoyl-AMP synthase-like domain / Telomere recombination / YrdC-like domain profile. / DHBP synthase / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Threonylcarbamoyl-AMP synthase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsHarris, K.A. / Bobay, B.G. / Sarachan, K.L. / Sims, A.F. / Bilbille, Y. / Deutsch, C. / Iwata-Reuyl, D. / Agris, P.F.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: NMR-based Structural Analysis of Threonylcarbamoyl-AMP Synthase and Its Substrate Interactions.
Authors: Harris, K.A. / Bobay, B.G. / Sarachan, K.L. / Sims, A.F. / Bilbille, Y. / Deutsch, C. / Iwata-Reuyl, D. / Agris, P.F.
History
DepositionDec 6, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Threonylcarbamoyl-AMP synthase


Theoretical massNumber of molelcules
Total (without water)20,6551
Polymers20,6551
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Threonylcarbamoyl-AMP synthase / TC-AMP synthase / L-threonylcarbamoyladenylate synthase / Ribosome maturation factor TsaC / t(6)A37 ...TC-AMP synthase / L-threonylcarbamoyladenylate synthase / Ribosome maturation factor TsaC / t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaC / tRNA threonylcarbamoyladenosine biosynthesis protein TsaC


Mass: 20655.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b3282, JW3243, rimN, tsaC, yrdC / Production host: Escherichia coli (E. coli)
References: UniProt: P45748, L-threonylcarbamoyladenylate synthase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HNCO
1713D H(CCO)NH
1813D C(CO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D 15N TOCSY-HSQC
11221H-15N HSQC-IPAP
11311H-15N TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] Recombinant TSAC protein, 10 % [U-100% 2H] D2O, 20 mM potassium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] Recombinant TSAC protein, 10 % [U-100% 2H] D2O, 20 mM potassium phosphate, 100 mM sodium chloride, 12 mg/mL Pf1 bacteriophage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRecombinant Yrdc protein-1[U-100% 13C; U-100% 15N]1
10 %D2O-2[U-100% 2H]1
20 mMpotassium phosphate-31
100 mMsodium chloride-41
1 mMRecombinant Yrdc protein-5[U-100% 13C; U-100% 15N]2
10 %D2O-6[U-100% 2H]2
20 mMpotassium phosphate-72
100 mMsodium chloride-82
12 mg/mLPf1 bacteriophage-92
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InovaVarianINOVA6001
Bruker Avance IIBrukerAVANCE II7002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1869 / Hydrogen bond constraints total count: 99
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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