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- PDB-2jqo: NMR solution structure of Bacillus subtilis YobA 21-120: Northeas... -

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Basic information

Entry
Database: PDB / ID: 2jqo
TitleNMR solution structure of Bacillus subtilis YobA 21-120: Northeast Structural Genomics Consortium target SR547
ComponentsHypothetical protein yobA
KeywordsSTRUCTURAL GENOMICS / Protein / OB-fold / beta barrel / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyProtein of unknown function DUF3221 / Protein of unknown function (DUF3221) / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta / Uncharacterized protein YobA
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics, simulated annealing
AuthorsCort, J.R. / Ramelot, T.A. / Chen, C.X. / Jang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Cort, J.R. / Ramelot, T.A. / Chen, C.X. / Jang, M. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR solution structure of Bacillus subtilis YobA 21-120: Northeast Structural Genomics Consortium target SR547
Authors: Cort, J.R.
History
DepositionJun 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _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
Revision 1.6May 8, 2024Group: Database references / Category: 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: Hypothetical protein yobA


Theoretical massNumber of molelcules
Total (without water)12,5281
Polymers12,5281
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 / 25lowest energy, fewest restraint violations, favorable non-bonded parameters
RepresentativeModel #1no selection bias was used

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Components

#1: Protein Hypothetical protein yobA


Mass: 12528.110 Da / Num. of mol.: 1 / Fragment: sequence database residues 21-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yobA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O31835

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D (H)CCH-TOCSY
1713D HNHA
1813D HNCO
1913D CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11234D 1H-13C-13C-1H HMQC-NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.75 mM [U-100% 13C; U-100% 15N] entity, 10 mM dithiothreitol, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.79 mM [U-100% N15]; 13C from 5% 13C-glucose in growth medium entity, 10 mM dithiothreitol, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
30.75 mM [U-100% 13C; U-100% 15N] entity, 10 mM dithiothreitol, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMentity[U-100% 13C; U-100% 15N]1
10 mMdithiothreitol1
5 mMcalcium chloride1
100 mMsodium chloride1
20 mMammonium acetate1
0.02 %sodium azide1
0.79 mMentity[U-100% N15]; 13C from 5% 13C-glucose in growth medium2
10 mMdithiothreitol2
5 mMcalcium chloride2
100 mMsodium chloride2
20 mMammonium acetate2
0.02 %sodium azide2
0.75 mMentity[U-100% 13C; U-100% 15N]3
10 mMdithiothreitol3
5 mMcalcium chloride3
100 mMsodium chloride3
20 mMammonium acetate3
0.02 %sodium azide3
Sample conditionspH: 4.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameDeveloperClassification
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
SparkyGoddarddata analysis
FelixAccelrys Software Inc.processing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
PSVSBhattacharya and Montelionestructure evaluation
RefinementMethod: torsion angle dynamics, molecular dynamics, simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: no selection bias was used
NMR ensembleConformer selection criteria: lowest energy, fewest restraint violations, favorable non-bonded parameters
Conformers calculated total number: 25 / Conformers submitted total number: 20

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