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- PDB-2l0c: Solution NMR Structure of protein STY4237 (residues 36-120) from ... -

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Basic information

Entry
Database: PDB / ID: 2l0c
TitleSolution NMR Structure of protein STY4237 (residues 36-120) from Salmonella enterica, Northeast Structural Genomics Consortium Target SlR115
ComponentsPutative membrane protein
KeywordsStructural Genomics / Unknown function / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-2 / Protein Structure Initiative
Function / homologyOB fold (Dihydrolipoamide Acetyltransferase, E2P) - #660 / Protein of unknown function DUF2500 / Protein of unknown function (DUF2500) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / membrane => GO:0016020 / Beta Barrel / Mainly Beta / DUF2500 domain-containing protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsCort, J.R. / Lee, D. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Ramelot, T.A. / Kennedy, M.A. ...Cort, J.R. / Lee, D. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Ramelot, T.A. / Kennedy, M.A. / Northeast Structural Genomics Consortium / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of protein STY4237 (residues 36-120) from Salmonella enterica, Northeast Structural Genomics Consortium Target SlR115
Authors: Cort, J. / Lee, D. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 30, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 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 1.3Jun 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 15, 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: Putative membrane protein


Theoretical massNumber of molelcules
Total (without water)11,1291
Polymers11,1291
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative membrane protein /


Mass: 11129.442 Da / Num. of mol.: 1 / Fragment: sequence database residues 36-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Gene: STY4237, t3948 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q8Z254

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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 HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D 1H-13C aliph NOESY
1813D 1H-15N NOESY
191(H)CCH-TOCSY
11013D HBHA(CO)NH
11113D C(CO)NH
11224D 1H-13C-13C-1H HMQC NOESY
11332D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] SlR115, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3, 10 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
21.1 mM [U-100% 13C; U-100% 15N] SlR115, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3, 100% D2O100% D2O
31.1 mM [5% 13C; U-100% 15N] SlR115, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMSlR115-1[U-100% 13C; U-100% 15N]1
100 mMNaCl-21
20 mMMES-31
5 mMCaCl2-41
0.05 %NaN3-51
10 mMDTT-61
1.1 mMSlR115-7[U-100% 13C; U-100% 15N]2
100 mMNaCl-82
20 mMMES-92
5 mMCaCl2-102
0.05 %NaN3-112
1.1 mMSlR115-12[5% 13C; U-100% 15N]3
100 mMNaCl-133
20 mMMES-143
5 mMCaCl2-153
0.05 %NaN3-163
Sample conditionspH: 6.5 / 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
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
REDCATValafar, Prestegardgeometry optimization
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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