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- PDB-2js1: Solution NMR structure of the homodimer protein YVFG from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 2js1
TitleSolution NMR structure of the homodimer protein YVFG from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR478
ComponentsUncharacterized protein yvfG
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / helical bundle / homodimer / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyHelix Hairpins - #40 / Uncharacterised domain YvfG / YvfG domain superfamily / YvfG protein / Helix Hairpins / Helix non-globular / Special / Uncharacterized protein YvfG
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMacnaughtan, M.A. / Weldeghiorghis, T. / Wang, X. / Bansal, S. / Tian, F. / Wang, D. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. ...Macnaughtan, M.A. / Weldeghiorghis, T. / Wang, X. / Bansal, S. / Tian, F. / Wang, D. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Prestegard, J.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Structure of the Bacillus subtilis Protein YvfG.
Authors: Macnaughtan, M.A. / Weldeghiorghis, T. / Wang, X. / Bansal, S. / Tian, F. / Wang, D. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T. ...Authors: Macnaughtan, M.A. / Weldeghiorghis, T. / Wang, X. / Bansal, S. / Tian, F. / Wang, D. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Prestegard, J.H.
History
DepositionJun 29, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name / _citation_author.name
Revision 1.4Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.5Jun 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 1.6May 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 yvfG
B: Uncharacterized protein yvfG


Theoretical massNumber of molelcules
Total (without water)19,1122
Polymers19,1122
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 yvfG


Mass: 9555.829 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yvfG, BSU34210 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P71066

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Solution Structure of B. subtilis protein SR478
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1412D 1H-13C HSQC ALIPH
1532D 1H-13C HSQC ALIPH 13C-Coupled
1613D (H)CCH-TOCSY
1713D CBCA(CO)NH
1813D 1H-13C NOESY ALIPH
1923D 1H-13C NOESY ALIPH NC-14N
11013D 1H-15N NOESY
11113D H(CCO)NH
11213D C(CO)NH
11313D 1H-13C NOESY aromatic
11412D 1H-13C HSQC aromatic
11512D 1H-15N HSQC NH2
11642D 1H-15N HSQC RDC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-13C; U-15N] protein, 10 mM Tris, 100 mM Sodium chloride, 0.02 % Sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-13C; U-15N] protein, 0.5 mM SR478, 10 mM Tris, 100 mM Sodium chloride, 0.02 % Sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.9 mM [U-5% 13C; U-15N] protein, 10 mM Tris, 100 mM Sodium chloride, 0.02 % Sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
40.6 mM [U-5% 13C; U-15N] protein, 10 mM Tris, 100 mM Sodium chloride, 0.02 % Sodium azide, 4 % Pentaethyleneglycol monodecyl ether/hexanol, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMSR478[U-13C; U-15N]1
10 mMTris1
100 mMSodium chloride1
0.02 %Sodium azide1
0.5 mMSR478-1[U-13C; U-15N]2
0.5 mMSR478-22
10 mMTris2
100 mMSodium chloride2
0.02 %Sodium azide2
0.9 mMSR478[U-5% 13C; U-15N]3
10 mMTris3
100 mMSodium chloride3
0.02 %Sodium azide3
0.6 mMSR478[U-5% 13C; U-15N]4
10 mMTris4
100 mMSodium chloride4
0.02 %Sodium azide4
4 %Pentaethyleneglycol monodecyl ether/hexanol4
Sample conditionspH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
PSVSBhattacharya and Montelionedata analysis
smartnotebook(Smartnotebook) Slupsky, Boyko, Booth, and Sykeschemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
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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