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- PDB-2k8y: Solution NMR Structure of Cgi121 from Methanococcus jannaschii. N... -

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Basic information

Entry
Database: PDB / ID: 2k8y
TitleSolution NMR Structure of Cgi121 from Methanococcus jannaschii. Northeast Structural Genomics Consortium Target MJ0187
ComponentsUncharacterized protein MJ0187
Keywordsstructural genomics / unknown function / regulatory subunit of the Bud32 kinase / component of the KEOPS complex / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyPF0523-like / CGI121/TPRKB / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / 2-Layer Sandwich / Alpha Beta / Regulatory protein Cgi121
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsRumpel, S. / Fares, C. / Neculai, D. / Arrowsmith, C. / Montelione, G.T. / Sicheri, F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Mol.Cell / Year: 2008
Title: Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine.
Authors: Mao, D.Y. / Neculai, D. / Downey, M. / Orlicky, S. / Haffani, Y.Z. / Ceccarelli, D.F. / Ho, J.S. / Szilard, R.K. / Zhang, W. / Ho, C.S. / Wan, L. / Fares, C. / Rumpel, S. / Kurinov, I. / ...Authors: Mao, D.Y. / Neculai, D. / Downey, M. / Orlicky, S. / Haffani, Y.Z. / Ceccarelli, D.F. / Ho, J.S. / Szilard, R.K. / Zhang, W. / Ho, C.S. / Wan, L. / Fares, C. / Rumpel, S. / Kurinov, I. / Arrowsmith, C.H. / Durocher, D. / Sicheri, F.
History
DepositionSep 25, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 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: Uncharacterized protein MJ0187


Theoretical massNumber of molelcules
Total (without water)17,0921
Polymers17,0921
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein MJ0187


Mass: 17092.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Genus: Methanococcus / Species: jannaschii / Gene: MJ0187 / Plasmid: pGEX / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: Q57646

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1713D HBHA(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: protein / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.1 / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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