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- PDB-2k3i: Solution NMR structure of protein yiiS from Shigella flexneri. No... -

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Basic information

Entry
Database: PDB / ID: 2k3i
TitleSolution NMR structure of protein yiiS from Shigella flexneri. Northeast Structural Genomics Consortium target SfR90
ComponentsUncharacterized protein yiiS
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / GFT NMR / Protein structure / PSI / NESG / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyConserved hypothetical protein CHP00743 / Protein of unknown function (DUF406) / Alpha-Beta Plaits - #860 / UPF0234-like, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesShigella flexneri 2a (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsMills, J.L. / Singarapu, K.K. / Eletsky, A. / Sukumaran, D.K. / Wang, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Liu, J. / Baran, M.C. ...Mills, J.L. / Singarapu, K.K. / Eletsky, A. / Sukumaran, D.K. / Wang, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2010
Title: Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175.
Authors: Singarapu, K.K. / Mills, J.L. / Xiao, R. / Acton, T. / Punta, M. / Fischer, M. / Honig, B. / Rost, B. / Montelione, G.T. / Szyperski, T.
History
DepositionMay 8, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Structure summary
Revision 1.3Apr 2, 2014Group: Source and taxonomy
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 yiiS


Theoretical massNumber of molelcules
Total (without water)12,0311
Polymers12,0311
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 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Uncharacterized protein yiiS


Mass: 12030.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Strain: Serotype 2a / Gene: yiiS, S3747, SF4000 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q83IT9, UniProt: A0A384LB29*PLUS

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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
1414,3 D GFT HNNACBCA
1514,3 D GFT CABCACONHN
1614,3D HABCAB(CO)NHN
1714,3D GFT (H)CCH COSY
1813D (H)CCH-COSY
1913D simNOESY
11022D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] SfR90, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21.02 mM [U-5% 13C; U-100% 15N] SfR90, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMSfR90[U-100% 13C; U-100% 15N]1
50 uMDSS1
1.02 mMSfR90[U-5% 13C; U-100% 15N]2
50 uMDSS2
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
XEASYBartels et al.data analysis
XEASYBartels et al.chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJVariancollection
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
PSVSBhattacharya and Montelionestructure solution
TALOSCornilescu, Delaglio and Baxstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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