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- PDB-2jmk: Solution structure of ta0956 -

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Basic information

Entry
Database: PDB / ID: 2jmk
TitleSolution structure of ta0956
ComponentsHypothetical protein Ta0956
KeywordsPROTEIN BINDING / Hypothetical Protein
Function / homologyThermoplasma acidophilum protein TA0956 / Thermoplasma acidophilum protein TA0956 / TA0956 superfamily / Thermoplasma acidophilum protein TA0956 / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesThermoplasma acidophilum (acidophilic)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKoo, B. / Jung, J. / Jung, H. / Nam, H. / Kim, Y. / Yee, A. / Arrowsmith, C.H. / Lee, W.
CitationJournal: Proteins / Year: 2007
Title: Solution structure of the hypothetical novel-fold protein TA0956 from Thermoplasma acidophilum
Authors: Koo, B.K. / Jung, J. / Jung, H. / Nam, H.W. / Kim, Y.S. / Yee, A. / Lee, W.
History
DepositionNov 20, 2006Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 1, 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

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Assembly

Deposited unit
A: Hypothetical protein Ta0956


Theoretical massNumber of molelcules
Total (without water)12,6301
Polymers12,6301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical protein Ta0956


Mass: 12629.563 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: ta0956 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HJL1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1212D 1H-15N HSQC
1322D 1H-13C HSQC
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HNCO
1713D HNCA
1823D (H)CCH-TOCSY
1923D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-98% 13C; U-98% 15N] ta0956, 20 mM sodium phosphate, 100 mM sodium chloride, 5 mM DTT, 0.01 w/v sodium azide, 0.01 w/v DSS, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM [U-98% 13C; U-98% 15N] ta0956, 20 mM sodium phosphate, 100 mM sodium chloride, 5 mM DTT, 0.01 w/v sodium azide, 0.01 w/v DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMta0956[U-98% 13C; U-98% 15N]1
20 mMsodium phosphate1
100 mMsodium chloride1
5 mMDTT1
0.01 w/vsodium azide1
0.01 w/vDSS1
1.5 mMta0956[U-98% 13C; U-98% 15N]2
20 mMsodium phosphate2
100 mMsodium chloride2
5 mMDTT2
0.01 w/vsodium azide2
0.01 w/vDSS2
Sample conditionsIonic strength: 373.15 / pH: 6.5 / Pressure: Ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AMXBrukerAMX8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1GUNTERTrefinement
CYANADelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XwinNMRBruker Biospincollection
SparkyGoddardstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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