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- PDB-2ma8: Solution NMR Structure of Salmonella typhimurium LT2 Secreted Pro... -

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Basic information

Entry
Database: PDB / ID: 2ma8
TitleSolution NMR Structure of Salmonella typhimurium LT2 Secreted Protein SrfN: Northeast Structural Genomics Consortium Target StR109
ComponentsPutative secreted protein
KeywordsStructural Genomics / Unknown Function / homodimer / PSI-Biology / alpha+beta / secreted protein / Northeast Structural Genomics Consortium / NESG
Function / homologyYdgH/BhsA/McbA-like domain / YdgH-like superfamily / YdgH/BhsA/McbA-like domain / Flavin-binding protein dodecin / Dodecin-like / Dodecin subunit-like / 2-Layer Sandwich / Alpha Beta / Secreted protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsfirst structure that meets the conformer selection criteria, model1
AuthorsCort, J.R. / Eletsky, A. / Adkins, J.N. / Burnet, M.C. / Parish, D. / Liu, K. / Sukumaran, D.K. / Jiang, M. / Cunningham, K. / Ma, T. ...Cort, J.R. / Eletsky, A. / Adkins, J.N. / Burnet, M.C. / Parish, D. / Liu, K. / Sukumaran, D.K. / Jiang, M. / Cunningham, K. / Ma, T. / Xiao, R. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Plos One / Year: 2014
Title: Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO.
Authors: Eletsky, A. / Michalska, K. / Houliston, S. / Zhang, Q. / Daily, M.D. / Xu, X. / Cui, H. / Yee, A. / Lemak, A. / Wu, B. / Garcia, M. / Burnet, M.C. / Meyer, K.M. / Aryal, U.K. / Sanchez, O. ...Authors: Eletsky, A. / Michalska, K. / Houliston, S. / Zhang, Q. / Daily, M.D. / Xu, X. / Cui, H. / Yee, A. / Lemak, A. / Wu, B. / Garcia, M. / Burnet, M.C. / Meyer, K.M. / Aryal, U.K. / Sanchez, O. / Ansong, C. / Xiao, R. / Acton, T.B. / Adkins, J.N. / Montelione, G.T. / Joachimiak, A. / Arrowsmith, C.H. / Savchenko, A. / Szyperski, T. / Cort, J.R.
History
DepositionJun 29, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 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 secreted protein
B: Putative secreted protein


Theoretical massNumber of molelcules
Total (without water)18,4542
Polymers18,4542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1521.5 Å2
ΔGint-4 kcal/mol
Surface area10755.3 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40low energy structures with few restraint violations and reasonable geometry
RepresentativeModel #1first structure that meets the conformer selection criteria

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Components

#1: Protein Putative secreted protein


Mass: 9227.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM0082 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q7CR88

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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 ali
1312D 1H-13C ct-HSQC ali
1412D 1H-13C HSQC aro
1512D 1H-13C ct-HSQC aro
1613D HNCO
171GFT (4,3)D CABCA(CO)NHN
181GFT (4,3)D HNNCABCA
191GFT (4,3)D HABCAB(CO)NHN
1101GFT (4,3)D (H)CCH-COSY ali
1111GFT (4,3)D (H)CCH-COSY aro
11213D 1H-13C/15N simNOESY
11333D 1H-13C X-filtered NOESY
11422D 1H-13C 28ms ct-HSQC
11522D 1H-13C 56ms ct-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.38 mM [U-100% 13C; U-100% 15N] StR109 subunit, 100 mM sodium chloride, 100 mM DTT, 5 mM CaCl2, 20 mM MES, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21.8 mM [U-5% 13C; U-100% 15N] StR109 subunit, 100 mM sodium chloride, 100 mM DTT, 5 mM CaCl2, 20 mM MES, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
31.2 mM [U-100% 13C; U-100% 15N] StR109 subunit, 1.2 mM StR109 subunit, 100 mM sodium chloride, 100 mM DTT, 5 mM CaCl2, 20 mM MES, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.38 mMStR109 subunit-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
100 mMDTT-31
5 mMCaCl2-41
20 mMMES-51
0.02 %sodium azide-61
1.8 mMStR109 subunit-7[U-5% 13C; U-100% 15N]2
100 mMsodium chloride-82
100 mMDTT-92
5 mMCaCl2-102
20 mMMES-112
0.02 %sodium azide-122
1.2 mMStR109 subunit-13[U-100% 13C; U-100% 15N]3
1.2 mMStR109 subunit-143
100 mMsodium chloride-153
100 mMDTT-163
5 mMCaCl2-173
20 mMMES-183
0.02 %sodium azide-193
Sample conditionsIonic strength: 115 / pH: 6.5 / Pressure: 1 atm / 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
NameVersionDeveloperClassification
CYANA2.1P.GUNTERT ET AL.structure solution
CYANA2.1P.GUNTERT ET AL.refinement
VNMR6.1CVariancollection
XEASY1.3.13Bartels et al.data analysis
AutoAssign1.15.1Zimmerman, Moseley, Kulikowski, Montelionechemical shift assignment
CARA1.5.5Keller et al.data analysis
PROSA6.0.2Guntertprocessing
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: first structure that meets the conformer selection criteria
NMR ensembleConformer selection criteria: low energy structures with few restraint violations and reasonable geometry
Conformers calculated total number: 40 / Conformers submitted total number: 20

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