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- PDB-1jdq: Solution Structure of TM006 Protein from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1jdq
TitleSolution Structure of TM006 Protein from Thermotoga maritima
ComponentsHYPOTHETICAL PROTEIN TM0983Hypothesis
KeywordsSTRUCTURAL GENOMICS / TM006 / Thermotoga maritima
Function / homologyTusA-like domain / Uncharacterized protein family UPF0033 signature. / TusA-like domain / Sulfurtransferase TusA / TusA-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta / Putative sulfur carrier protein TM_0983
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsDenisov, A.Y. / Finak, G. / Yee, A. / Kozlov, G. / Gehring, K. / Arrowsmith, C.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: An NMR approach to structural proteomics.
Authors: Yee, A. / Chang, X. / Pineda-Lucena, A. / Wu, B. / Semesi, A. / Le, B. / Ramelot, T. / Lee, G.M. / Bhattacharyya, S. / Gutierrez, P. / Denisov, A. / Lee, C.H. / Cort, J.R. / Kozlov, G. / ...Authors: Yee, A. / Chang, X. / Pineda-Lucena, A. / Wu, B. / Semesi, A. / Le, B. / Ramelot, T. / Lee, G.M. / Bhattacharyya, S. / Gutierrez, P. / Denisov, A. / Lee, C.H. / Cort, J.R. / Kozlov, G. / Liao, J. / Finak, G. / Chen, L. / Wishart, D. / Lee, W. / McIntosh, L.P. / Gehring, K. / Kennedy, M.A. / Edwards, A.M. / Arrowsmith, C.H.
History
DepositionJun 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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
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 TM0983


Theoretical massNumber of molelcules
Total (without water)11,2221
Polymers11,2221
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 85structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein HYPOTHETICAL PROTEIN TM0983 / Hypothesis / TM006 Protein


Mass: 11221.925 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: Pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold magic / References: UniProt: Q9X078

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB
121cbca(co)hn
23215N-HMQC-TOCSY
24215N-HMQC-NOESY
353TOCSY
363NOESY
NMR detailsText: Structure was determined using 2D and 3D experiments for unlabelled, 15N-labelled and double-labelled protein.

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM TM006 protein U-15N,13C; 50mM phosphate buffer90% H2O/10% D2O
22 mM TM006 protein U-15N; 50mM phosphate buffer90% H2O/10% D2O
35 mM TM006 unlabelled protein; 50mM phosphate buffer90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1150 mM NaCl 6.8 1 atm310 K
2150 mM NaCl 6.8 1 atm310 K
3150 mM NaCl 6.8 1 atm310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1BRUKERcollection
XwinNMR2.1BRUKERprocessing
XEASY1.3.13Bartels et al.data analysis
ARIA14.5.98Nilges et al.data analysis
CNS0.9Brunger et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: After determination of protein fold by using manual NOE assigments, values of coupling constants and 13C chemical shifts, automatic peak NOE assigments were made by using ARIA and the ...Details: After determination of protein fold by using manual NOE assigments, values of coupling constants and 13C chemical shifts, automatic peak NOE assigments were made by using ARIA and the structure refined by using standard protocol in CNS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 85 / Conformers submitted total number: 20

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