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- PDB-2k5e: SOLUTION STRUCTURE OF PUTATIVE UNCHARACTERIZED PROTEIN GSU1278 FR... -

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Basic information

Entry
Database: PDB / ID: 2k5e
TitleSOLUTION STRUCTURE OF PUTATIVE UNCHARACTERIZED PROTEIN GSU1278 FROM METHANOCALDOCOCCUS JANNASCHII, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET GsR195
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / Helix protein / Structural Genomic / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyConserved hypothetical protein CHP03980, redox-disulphide / SP0561-like / SP0561-like / Domain of unknown function DUF1858 / ScdA-like, N-terminal domain superfamily / Domain of unknown function (DUF1858) / Orthogonal Bundle / Mainly Alpha / DUF1858 domain-containing protein
Function and homology information
Biological speciesMethanococcus jannaschii (archaea)
MethodSOLUTION NMR / simulated annealing, distance geometry, torsion angle dynamics
AuthorsLiu, G. / Zhao, L. / Ciccosanti, C. / Jiang, M. / Xiao, R. / Swapna, G. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. ...Liu, G. / Zhao, L. / Ciccosanti, C. / Jiang, M. / Xiao, R. / Swapna, G. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: SOLUTION STRUCTURE OF PUTATIVE UNCHARACTERIZED PROTEIN GSU1278 FROM METHANOCALDOCOCCUS JANNASCHII, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET GsR195
Authors: LIU, G. / XIAO, R. / Montelione, G.T.
History
DepositionJun 27, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)8,0121
Polymers8,0121
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 uncharacterized protein


Mass: 8012.005 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus jannaschii (archaea) / Species: jannaschii / Plasmid: pET 21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: Q74DN8*PLUS

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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
1322D 1H-13C HSQC
1413D SIMULTANEOUS CN-NOESY
1514,3D GFT CABCACONHN
1614,3D GFT HNNCABCA
1714,3D GFT HABCAB(CO)NHN
1813D HNCO
1913D CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.11 mM [U-100% 13C; U-100% 15N] protein, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21.48 mM [U-10% 13C; U-100% 15N] protein, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.11 mMprotein[U-100% 13C; U-100% 15N]1
50 uMDSS1
1.48 mMprotein[U-10% 13C; U-100% 15N]2
50 uMDSS2
Sample conditionsIonic strength: na / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.2.1Huang, Tejero, Powers and Montelionepeak picking
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASY1.3.1Bartels et al.data analysis
TopSpinBruker Biospincollection
VnmrJVariancollection
RefinementMethod: simulated annealing, distance geometry, 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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