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- PDB-2dsm: NMR Structure of Bacillus Subtilis Protein YqaI, Northeast Struct... -

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Basic information

Entry
Database: PDB / ID: 2dsm
TitleNMR Structure of Bacillus Subtilis Protein YqaI, Northeast Structural Genomics Target SR450
ComponentsHypothetical protein yqaI
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / homodimer / domain swapped dimer / inter-domain beta sheet / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyYqaI domain / Uncharacterised protein family YqaI / YqaI domain superfamily / Hypothetical protein Yqai / Herpes Virus-1 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein YqaI
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR
AuthorsRamelot, T.A. / Cort, J.R. / Wang, D. / Janua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. ...Ramelot, T.A. / Cort, J.R. / Wang, D. / Janua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: to be published
Title: NMR Structure of Bacillus Subtilis Protein YqaI, Northeast Structural Genomics Target SR450
Authors: Ramelot, T.A. / Cort, J.R. / Wang, D. / Janua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJul 1, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yqaI
B: Hypothetical protein yqaI


Theoretical massNumber of molelcules
Total (without water)17,3072
Polymers17,3072
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Hypothetical protein yqaI


Mass: 8653.513 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yqaI or BSU26300 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (Lamda DE3) pMGK / References: UniProt: P45906

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1323D 13C-separated NOESY
1424D 13C/15N-separated NOESY
153HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM YqaI, U-15N, 13C; 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 95% D2O, 5% D2O95% D2O, 5% D2O
21.0mM YqaI, U-15N, 13C; 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 100% D2O100% D2O
31.4mM YqaI, U-15N, 5%-13C, 20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 0.02% NaN3, 95% D2O, 5% D2O95% D2O, 5% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 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
NameVersionClassification
Sparky3.1data analysis
NMRPipeLinux9processing
X-PLORxplor-nih-2.11.2refinement
CNS1.1refinement
VNMR6.1Ccollection
AutoStructure2.1.1data analysis
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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