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- PDB-2jw1: Structural characterization of the type III pilotin-secretin inte... -

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Basic information

Entry
Database: PDB / ID: 2jw1
TitleStructural characterization of the type III pilotin-secretin interaction in Shigella flexneri by NMR spectroscopy
Components
  • Lipoprotein mxiM
  • Outer membrane protein mxiD
KeywordsMEMBRANE PROTEIN / protein-protein interaction / Lipoprotein / Membrane / Outer membrane / Palmitate / Plasmid / Virulence / Protein transport / Transport
Function / homology
Function and homology information


type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / cell outer membrane
Similarity search - Function
Pilot protein MxiM / Pilot protein MxiM / MxiM superfamily / Pilot protein MxiM / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : ...Pilot protein MxiM / Pilot protein MxiM / MxiM superfamily / Pilot protein MxiM / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / : / NolW-like / NolW-like superfamily / Bacterial type II/III secretion system short domain / Type II/III secretion system / Bacterial type II and III secretion system protein / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Type 3 secretion system pilotin / Type 3 secretion system secretin
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsOkon, M.S. / Lario, P.I. / Creagh, L. / Jung, Y.M.T. / Maurelli, A.T. / Strynadka, N.C.J. / McIntosh, L.P.
CitationJournal: Structure / Year: 2008
Title: Structural Characterization of the Type-III Pilot-Secretin Complex from Shigella flexneri
Authors: Okon, M. / Moraes, T.F. / Lario, P.I. / Creagh, A.L. / Haynes, C.A. / Strynadka, N.C. / McIntosh, L.P.
History
DepositionOct 2, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _pdbx_database_status.status_code_cs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoprotein mxiM
B: Outer membrane protein mxiD


Theoretical massNumber of molelcules
Total (without water)15,0352
Polymers15,0352
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Lipoprotein mxiM


Mass: 12903.888 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: mxiM / Production host: Escherichia coli (E. coli) / References: UniProt: P0A1X2
#2: Protein/peptide Outer membrane protein mxiD


Mass: 2131.315 Da / Num. of mol.: 1 / Fragment: sequence database residues 549-566 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q04641
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HNCA
1513D HN(CO)CA
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
19113C/15N F1,F2-filtered NOESY
110113C/15N F1,F2-filtered TOCSY

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Sample preparation

DetailsContents: 0.3 -0.5 mM [U-95% 13C; U-95% 15N] MxiM(28-142), 0.5 - 0.7 mM MxiD(553-570), 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMMxiM(28-142)[U-95% 13C; U-95% 15N]1
0.5 mMMxiD(553-570)1
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.0.4Johnson, One Moon Scientificprocessing
ARIA2.1Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: Additional water refinement was made for each of submitted conformers
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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