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- PDB-1jw3: Solution Structure of Methanobacterium Thermoautotrophicum Protei... -

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Basic information

Entry
Database: PDB / ID: 1jw3
TitleSolution Structure of Methanobacterium Thermoautotrophicum Protein 1598. Ontario Centre for Structural Proteomics target MTH1598_1_140; Northeast Structural Genomics Target TT6
ComponentsConserved Hypothetical Protein MTH1598
KeywordsStructural Genomics / Unknown Function / MTH1598 / hypothetical protein / Protein Structure Initiative / OCSP / NESG / beta-alpha-beta sandwich fold / PSI / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


tRNA splicing, via endonucleolytic cleavage and ligation / calcium ion binding
Similarity search - Function
Archease, archaea / Archease, Possible Chaperone; Chain: A; domain 1 / Archease domain / Archease / Archease domain / Archease domain superfamily / Archease protein family (MTH1598/TM1083) / 3-Layer(bab) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsChang, X. / Connelly, G. / Yee, A. / 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
DepositionSep 2, 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: 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: Conserved Hypothetical Protein MTH1598


Theoretical massNumber of molelcules
Total (without water)16,2021
Polymers16,2021
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)10 / 50structures with the lowest energy
Representative

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Components

#1: Protein Conserved Hypothetical Protein MTH1598


Mass: 16202.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter thermautotrophicus (archaea)
Plasmid: PET15B / References: UniProt: O27635

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C-separated NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY

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Sample preparation

DetailsContents: 2mM MTH1598 U-15N,13C
Solvent system: 300 mM NaCl,10 mM Phosphate, 10% D2O, pH 6.5
Sample conditionsIonic strength: 300 mM NaCl / 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
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA5004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2000.02.14Delagioprocessing
Sparky3.95Goddarddata analysis
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1347 restraints, 1157 are NOE-derived distance constraints, 190 dihedral angle restraints.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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