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- PDB-2jpu: solution structure of NESG target SsR10, Orf c02003 protein -

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Basic information

Entry
Database: PDB / ID: 2jpu
Titlesolution structure of NESG target SsR10, Orf c02003 protein
ComponentsOrf c02003 protein
KeywordsSTRUCTURAL GENOMICS / solution structure / ssr10 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyArchaeal PaREP1 / Archaeal PaREP1/PaREP8 family / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Orf c02003 protein
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsWu, Y. / Singarapu, K.K. / Zhang, Q. / Eletski, A. / Xu, D. / Sukumaran, D. / Parish, D. / Wang, D. / Jiang, M. / Cunningham, K. ...Wu, Y. / Singarapu, K.K. / Zhang, Q. / Eletski, A. / Xu, D. / Sukumaran, D. / Parish, D. / Wang, D. / Jiang, M. / Cunningham, K. / Maglaqui, M. / Owens, L. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T. / Rost, B. / Montelione, G. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution structure of NESG target SsR10, Orf c02003 protein
Authors: Wu, Y. / Singarapu, K.K. / Zhang, Q. / Eletski, A. / Xu, D. / Sukumaran, D. / Parish, D. / Wang, D. / Jiang, M. / Cunningham, K. / Maglaqui, M. / Owens, L. / Xiao, R. / Liu, J. / Baran, M. / ...Authors: Wu, Y. / Singarapu, K.K. / Zhang, Q. / Eletski, A. / Xu, D. / Sukumaran, D. / Parish, D. / Wang, D. / Jiang, M. / Cunningham, K. / Maglaqui, M. / Owens, L. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T. / Rost, B. / Montelione, G. / Szyperski, T.
History
DepositionMay 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.4Jun 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 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Orf c02003 protein


Theoretical massNumber of molelcules
Total (without water)15,0841
Polymers15,0841
Non-polymers00
Water0
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 Orf c02003 protein / Hypothetical protein


Mass: 15084.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: orf c02003 / Production host: Escherichia coli (E. coli) / References: UniProt: P95883

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114,3D, GFT HNNCABCA
1214,3D, GFT CABCACONNH
1314,3D, GFT (H)CCH COSY
1413D, 15N-13C RESOLVED SIMULTANIOUS NOESY
1513D HNCO
1612D 1H-15N HSQC
1722D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM protein, 95% H2O/5% D2O95% H2O/5% D2O
21.0 mM protein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.1 mMentity1
1.0 mMentity2
Sample conditionsIonic strength: 100mM / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
RefinementMethod: simulated annealing / 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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