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- PDB-2js5: NMR Structure of protein Q60C73_METCA. Northeast Structural Genom... -

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Basic information

Entry
Database: PDB / ID: 2js5
TitleNMR Structure of protein Q60C73_METCA. Northeast Structural Genomics Consortium target McR1
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / homodimer / protein structure / NMR spectroscopy / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyPutative nitrogen fixation protein / Rop-like / Helix hairpin bin / Helix hairpin bin domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesMethylococcus capsulatus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSingarapu, K.K. / Wu, Y. / Eletsky, A. / Sukumaran, D. / Parish, D. / Chen, C.X. / Nwosu, C. / Maglaqui, M. / Xiao, R. / Liu, J. ...Singarapu, K.K. / Wu, Y. / Eletsky, A. / Sukumaran, D. / Parish, D. / Chen, C.X. / Nwosu, C. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Structure of protein Q60C73_METCA.
Authors: Singarapu, K.K. / Wu, Y. / Eletsky, A. / Sukumaran, D. / Parish, D. / Chen, C.X. / Nwosu, C. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / ...Authors: Singarapu, K.K. / Wu, Y. / Eletsky, A. / Sukumaran, D. / Parish, D. / Chen, C.X. / Nwosu, C. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 29, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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 1.3Jun 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
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,5372
Polymers16,5372
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 8268.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (bacteria) / Strain: Bath, NCIMB 11132 / Gene: MCA0237 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60C73

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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 HN(CA)CB
1413D CBCA(CO)NH
1513D (H)CCH-COSY
1614,3D GFT HABCABCONH
1713D sim NOESY
1823D giltered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-50% 13C; U-50% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMprotein[U-100% 13C; U-100% 15N]1
1.0 mMprotein[U-50% 13C; U-50% 15N]2
Sample conditionsIonic strength: 100 / 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
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
AutoAssignHuang, Tejero, Powers and Montelionechemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
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: 20

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