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- PDB-1ryj: Solution NMR Structure of Protein Mth1743 from Methanobacterium t... -

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Basic information

Entry
Database: PDB / ID: 1ryj
TitleSolution NMR Structure of Protein Mth1743 from Methanobacterium thermoautotrophicum. Ontario Centre for Structural Proteomics target MTH1743_1_70; Northeast Structural Genomics Consortium Target TT526.
Componentsunknown
Keywordsstructural genomics / unknown function / beta/alpha protein / Protein Structure Initiative / OCSP / NESG / PSI / Northeast Structural Genomics Consortium
Function / homologySulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta / MoaD/ThiS family protein
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus (archaea)
MethodSOLUTION NMR / torsion angle dyanmics simulated annealing restrained molecular dynamic simulations
AuthorsYee, A. / Chang, X. / Pineda-Lucena, A. / Wu, B. / Semesi, A. / Le, B. / Ramelot, T. / Lee, G.M. / Bhattacharyya, S. / Gutierrez, P. ...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. / Northeast Structural Genomics Consortium (NESG)
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
DepositionDec 22, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 24, 2004ID: 1jsb
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: unknown


Theoretical massNumber of molelcules
Total (without water)7,7651
Polymers7,7651
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 unknown / hypothetical protein mth1743


Mass: 7765.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermococcus thermolithotrophicus (archaea)
Gene: archaea / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O27775

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 13C,15N-simultaneous NOESY

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Sample preparation

DetailsContents: 1mM mth1743, 450 mM NaCl, 25 mM Na2PO4, 1mM Benzamidine, 1xinhibitor cooktail, 0.01% NaN3, pH 6.5
Solvent system: 95% H2O/5% D2O

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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
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglio, F.processing
DYANA1.5Gunter,P.structure solution
CNS1refinement
RefinementMethod: torsion angle dyanmics simulated annealing restrained molecular dynamic simulations
Software ordinal: 1
Details: 1496 NOE-derived distance constraints, 103 dihedral angle constraints, 34 hydrogen bonds
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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