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- PDB-2lv4: ZirS C-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 2lv4
TitleZirS C-terminal Domain
ComponentsPutative outer membrane or exported protein
KeywordsPROTEIN BINDING / Antivirulence / Adhesion
Function / homologyZinc-regulated secreted antivirulence protein, C-terminal / Zinc-regulated secreted antivirulence protein C-terminal domain / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Outer membrane or exported protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodSOLUTION NMR / simulated annealing, distance geometry
Model detailsclosest to the average, model 8
AuthorsPrehna, G. / Li, Y. / Stoynov, N. / Okon, M. / Vukovic, M. / Mcintosh, L.P. / Foster, L.J. / Finlay, B. / Strynadka, N.C.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The zinc regulated antivirulence pathway of salmonella is a multiprotein immunoglobulin adhesion system.
Authors: Prehna, G. / Li, Y. / Stoynov, N. / Okon, M. / Vuckovic, M. / McIntosh, L.P. / Foster, L.J. / Finlay, B.B. / Strynadka, N.C.
History
DepositionJun 28, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: 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
Remark 700 SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative outer membrane or exported protein


Theoretical massNumber of molelcules
Total (without water)16,1051
Polymers16,1051
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)10 / 10target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Putative outer membrane or exported protein


Mass: 16105.110 Da / Num. of mol.: 1 / Fragment: C-terminal residues 136-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: STM1668 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZP79

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D HNCO
141HN(CA)CO
1512D 1H-15N HSQC
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
191CCC-TOCSY-NNH
1101CT-HSQC
1111(HB)CB(CGCD)HD aromatic
1121HBCBGCCC-TOCSY
1131HCC-TOCSY-NNH

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] ZirS, 50 mM TRIS, 50 mM sodium chloride, 0.1 mM TCEP, 0.1 mM PMSF, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMZirS-1[U-100% 13C; U-100% 15N]1
50 mMTRIS-21
50 mMsodium chloride-31
0.1 mMTCEP-41
0.1 mMPMSF-51
Sample conditionsIonic strength: 0.05 / pH: 7.1 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY5001
Varian UnityVarianUNITY6002

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxgeometry optimization
TALOSCornilescu, Delaglio and Baxstructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, distance geometry / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 10 / Conformers submitted total number: 10

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