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- PDB-2k9f: Structural features of the complex between the DsbD N-terminal an... -

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Basic information

Entry
Database: PDB / ID: 2k9f
TitleStructural features of the complex between the DsbD N-terminal and the PilB N-terminal domains from Neisseria meningitidis
Components
  • Thiol:disulfide interchange protein dsbD
  • Thioredoxin
KeywordsOXIDOREDUCTASE / protein / docking / thioredoxin / immunoglobulin / DsbD / PilB / Electron transport / Multifunctional enzyme / Redox-active center / Transport / Cytochrome c-type biogenesis / Inner membrane / Membrane / NAD / Transmembrane
Function / homology
Function and homology information


L-methionine:thioredoxin-disulfide S-oxidoreductase activity / peptide-methionine (R)-S-oxide reductase / protein-disulfide reductase / peptide-methionine (R)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein repair / protein-disulfide reductase (NAD(P)H) activity / cytochrome complex assembly / protein-disulfide reductase activity ...L-methionine:thioredoxin-disulfide S-oxidoreductase activity / peptide-methionine (R)-S-oxide reductase / protein-disulfide reductase / peptide-methionine (R)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein repair / protein-disulfide reductase (NAD(P)H) activity / cytochrome complex assembly / protein-disulfide reductase activity / cell redox homeostasis / protein modification process / response to oxidative stress / electron transfer activity / plasma membrane / cytoplasm
Similarity search - Function
Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / Thiol:disulphide interchange protein DsbD / DsbD gamma / Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal / Cytochrome C biogenesis protein, transmembrane domain / Cytochrome C biogenesis protein transmembrane region / Peptide methionine sulfoxide reductase MsrB / Peptide methionine sulphoxide reductase MrsB domain ...Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / Thiol:disulphide interchange protein DsbD / DsbD gamma / Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal / Cytochrome C biogenesis protein, transmembrane domain / Cytochrome C biogenesis protein transmembrane region / Peptide methionine sulfoxide reductase MsrB / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Peptide methionine sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / Thioredoxin-like domain / Mss4-like superfamily / Redoxin / Redoxin / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Peptide methionine sulfoxide reductase MsrA/MsrB / Thiol:disulfide interchange protein DsbD
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup A (bacteria)
Neisseria meningitidis serogroup B (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsDocking using HADDOCK2.0 with ambiguous and unambiguous NMR restraints
AuthorsQuinternet, M. / Tsan, P. / Selme, L. / Jacob, C. / Boschi-Muller, S. / Branlant, G. / Cung, M.
CitationJournal: Structure / Year: 2009
Title: Formation of the complex between DsbD and PilB N-terminal domains from Neisseria meningitidis necessitates an adaptability of nDsbD.
Authors: Quinternet, M. / Tsan, P. / Selme-Roussel, L. / Jacob, C. / Boschi-Muller, S. / Branlant, G. / Cung, M.T.
History
DepositionOct 9, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin
B: Thiol:disulfide interchange protein dsbD


Theoretical massNumber of molelcules
Total (without water)30,0172
Polymers30,0172
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 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Thioredoxin


Mass: 15848.090 Da / Num. of mol.: 1 / Fragment: sequence database residues 34-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup A (bacteria)
Gene: msrAB, pilB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JWM8
#2: Protein Thiol:disulfide interchange protein dsbD / Protein-disulfide reductase / Disulfide reductase


Mass: 14168.737 Da / Num. of mol.: 1 / Fragment: sequence database residues 20-146 / Mutation: C102S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: dsbD / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JYM0, protein-disulfide reductase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Docking using HADDOCK2.0 with ambiguous and unambiguous NMR restraints
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1442D 1H-15N HSQC
1513D CBCA(CO)NH
1623D CBCA(CO)NH
1733D CBCA(CO)NH
1843D CBCA(CO)NH
1913D HNCO
11023D HNCO
11133D HNCO
11243D HNCO
11313D HNCA
11423D HNCA
11533D HNCA
11643D HNCA
11713D HN(CA)CB
11823D HN(CA)CB
11933D HN(CA)CB
12043D HN(CA)CB
12113D HN(CO)CA
12223D HN(CO)CA
12333D HN(CO)CA
12443D HN(CO)CA
12533D HNHA
12643D HNHA
12733D (H)CCH-TOCSY
12843D (H)CCH-TOCSY
12933D 1H-15N NOESY
13043D 1H-15N NOESY
13133D 1H-13C NOESY
13243D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.75 mM [U-13C; U-15N; U-2H] NterPilB, 0.75 mM nDsbD, 20 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
20.75 mM [U-13C; U-15N; U-2H] nDsbD, 0.75 mM NterPilB, 20 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
30.75 mM [U-100% 13C; U-100% 15N] NterPilB, 0.75 mM nDsbD, 20 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
40.75 mM [U-100% 13C; U-100% 15N] nDsbD, 0.75 mM NterPilB, 20 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMNterPilB[U-13C; U-15N; U-2H]1
0.5 mMnDsbD1
20 mMpotassium phosphate1
0.5 mMnDsbD[U-13C; U-15N; U-2H]2
0.5 mMNterPilB2
20 mMpotassium phosphate2
0.5 mMNterPilB[U-100% 13C; U-100% 15N]3
0.5 mMnDsbD3
20 mMpotassium phosphate3
0.5 mMnDsbD[U-100% 13C; U-100% 15N]4
0.5 mMNterPilB4
20 mMpotassium phosphate4
Sample conditionsIonic strength: 20 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
HADDOCK2Bonvin AmJJstructure solution
HADDOCK2Bonvin AmJJrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 10

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