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- PDB-2mbt: NMR study of PaDsbA -

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Basic information

Entry
Database: PDB / ID: 2mbt
TitleNMR study of PaDsbA
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / DsbA / oxidised / Structural Genomics
Function / homology
Function and homology information


disulfide oxidoreductase activity / periplasmic space
Similarity search - Function
Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / water refinement
Model detailsclosest to the average, model15
AuthorsRimmer, K. / Mohanty, B. / Scanlon, M.J.
CitationJournal: PLoS ONE / Year: 2017
Title: Fragment library screening identifies hits that bind to the non-catalytic surface of Pseudomonas aeruginosa DsbA1.
Authors: Mohanty, B. / Rimmer, K. / McMahon, R.M. / Headey, S.J. / Vazirani, M. / Shouldice, S.R. / Coincon, M. / Tay, S. / Morton, C.J. / Simpson, J.S. / Martin, J.L. / Scanlon, M.J.
History
DepositionAug 3, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / 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_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: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)21,1521
Polymers21,1521
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 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21152.260 Da / Num. of mol.: 1 / Fragment: unp residues 23-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: dsbA, PA5489 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Gold / References: UniProt: P0C2B2

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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 aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 2 mM [U-100% 13C; U-100% 15N] PaDsbA, 50 mM sodium phosphate, 50 mM sodium chloride, 0.02 % sodium azide, 10 % [U-100% 2H] D2O, 1 mM DSS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMPaDsbA-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
50 mMsodium chloride-31
0.02 %sodium azide-41
10 %D2O-5[U-100% 2H]1
1 mMDSS-61
Sample conditionsIonic strength: 50 mM sodium chloride / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
UNIOHerrmann, Guntert and Wuthrichchemical shift assignment
RefinementMethod: water refinement / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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