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- PDB-2aby: Solution structure of TA0743 from Thermoplasma acidophilum -

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Basic information

Entry
Database: PDB / ID: 2aby
TitleSolution structure of TA0743 from Thermoplasma acidophilum
Componentshypothetical protein TA0743
KeywordsUNKNOWN FUNCTION / helix-turn-helix
Function / homologyUncharacterised protein PF09406, DUF2004 / Protein of unknown function DUF2004 / Protein of unknown function (DUF2004) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesThermoplasma acidophilum (acidophilic)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsKim, B. / Jung, J. / Hong, E. / Yee, A. / Arrowsmith, C.H. / Lee, W.
CitationJournal: Proteins / Year: 2006
Title: NMR structure of the conserved novel-fold protein TA0743 from Thermoplasma acidophilum.
Authors: Kim, B. / Jung, J. / Hong, E. / Yee, A. / Arrowsmith, C.H. / Lee, W.
History
DepositionJul 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein TA0743


Theoretical massNumber of molelcules
Total (without water)17,3991
Polymers17,3991
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 #1

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Components

#1: Protein hypothetical protein TA0743


Mass: 17398.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HK62

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA

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Sample preparation

DetailsContents: 1.6mM TA0743 U-15N,13C,15N/13C 50mM Potassium phosphate buffer ,NaN3,90% H20,10% D20
Solvent system: 90% H20,10% D20
Sample conditionsIonic strength: no salt / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX5002
Varian UNITYPLUSVarianUNITYPLUS6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglioprocessing
Sparky3.11Goddard and Knellerdata analysis
MARS1.1Jung and Zweckstetterdata analysis
CYANA2Herrmannstructure solution
CYANA2Herrmannrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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