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- PDB-2kt6: Structural homology between the C-terminal domain of the PapC ush... -

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Basic information

Entry
Database: PDB / ID: 2kt6
TitleStructural homology between the C-terminal domain of the PapC usher and its plug
ComponentsOuter membrane usher protein papC
KeywordsTRANSPORT PROTEIN / Pilus / chaperone-usher / Gram-negative / Cell membrane / Cell outer membrane / Disulfide bond / Fimbrium biogenesis / Membrane / Transmembrane / Transport
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / cell outer membrane / identical protein binding
Similarity search - Function
PapC, C-terminal domain / Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain ...PapC, C-terminal domain / Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. / PapC-like, C-terminal domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer membrane usher protein PapC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsFord, B. / Rego, A. / Ragan, T.J. / Pinkner, J. / Dodson, K. / Driscoll, P.C. / Hultgren, S. / Waksman, G.
CitationJournal: J.Bacteriol. / Year: 2010
Title: Structural Homology between the C-Terminal Domain of the PapC Usher and Its Plug.
Authors: Ford, B. / Rego, A.T. / Ragan, T.J. / Pinkner, J. / Dodson, K. / Driscoll, P.C. / Hultgren, S. / Waksman, G.
History
DepositionJan 19, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane usher protein papC


Theoretical massNumber of molelcules
Total (without water)9,0711
Polymers9,0711
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)10 / 100Lowest Energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Outer membrane usher protein papC


Mass: 9071.371 Da / Num. of mol.: 1 / Fragment: sequence database residues 752-836
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: papC / Production host: Escherichia coli (E. coli) / References: UniProt: P07110

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCA
1323D HN(CO)CA
1423D HNCO
152HN(Ca)Co
162CbCa(Co)NH
1723D HN(CA)CB
1813D 1H-15N TOCSY short
1913D 1H-15N TOCSY long
11023D (H)CCH-TOCSY
1122TSNoesy N
11323D 1H-13C NOESY
11423D HN(CO)CA
1152CBCA(CO)NH
11612D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM MES, 20 mM sodium chloride, 300-500 mM [U-15N] CTD_Actual, 95% H2O/5% D2O95% H2O/5% D2O
220 mM MES, 20 mM sodium chloride, 300-500 mM [U-15N, U-13C] CTD_Actual, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
20 mMMES-11
20 mMsodium chloride-21
mMCTD_Actual-3[U-15N]300-5001
20 mMMES-42
20 mMsodium chloride-52
mMCTD_Actual-6[U-15N]300-5002
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Varian UnityVarianUNITY6002
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE7004

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.1CCPNchemical shift assignment
CcpNmr Analysis2.1CCPNpeak picking
DANGLE1.11data analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1 / Details: Xplor-NIH
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Lowest Energy / Conformers calculated total number: 100 / Conformers submitted total number: 10

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