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- PDB-5tlq: Model structure of the oxidized PaDsbA1 and 3-[(2-methylbenzyl)su... -

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Basic information

Entry
Database: PDB / ID: 5tlq
TitleModel structure of the oxidized PaDsbA1 and 3-[(2-methylbenzyl)sulfanyl]-4H-1,2,4-triazol-4-amine complex
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / oxidised PaDsbA1 / 3-((2-methylbenzyl)thio)-4H-1 / 2 / 4-triazol-4-amine / HADDOCK docking
Function / homology
Function and homology information


cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded 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 ...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
Chem-1YO / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMohanty, B. / Rimmer, K.A. / McMahon, R.M. / Headey, S.J. / Vazirani, M. / Shouldice, S.R. / Coincon, M. / Tay, S. / Morton, C.J. / Simpson, J.S. ...Mohanty, B. / Rimmer, K.A. / 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.S.
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
DepositionOct 11, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionApr 12, 2017ID: 2MBU
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3732
Polymers21,1521
Non-polymers2201
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21152.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: dsbA, PA5489 / Plasmid: pET28a / Cell line (production host): BL21(DE3)-Gold / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0C2B2
#2: Chemical ChemComp-1YO / 3-[(2-methylbenzyl)sulfanyl]-4H-1,2,4-triazol-4-amine


Mass: 220.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4S
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
131isotropic13D F1-13C,15N filtered F3-13Cedited [1H,1H]-NOESY

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Sample preparation

DetailsType: solution
Contents: 0.3 mM [U-98% 13C; U-98% 15N] PaDsbA1, 3.3 mM 3-((2-methylbenzyl)thio)-4H-1,2,4-triazol-4-amine, 97.3%D2O+1.7%D6-DMSO
Details: 300 uM PaDsbA1; 3.3 mM 3-((2-methylbenzyl)thio)-4H-1,2,4-triazol-4-amine; 1.7% D6-DMSO; 50 mM sodium Phosphate; 50 mM sodium Chloride; 0.02% sodium azide
Label: [U-13C,15N] PaDsbA1 and unlabelled 3-((2-methylbenzyl)thio)-4H-1,2,4-triazol-4-amine
Solvent system: 97.3%D2O+1.7%D6-DMSO
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMPaDsbA1[U-98% 13C; U-98% 15N]1
3.3 mM3-((2-methylbenzyl)thio)-4H-1,2,4-triazol-4-aminenatural abundance1
Sample conditionsDetails: 300 uM PaDsbA1; 3.3 mM 3-((2-methylbenzyl)thio)-4H-1,2,4-triazol-4-amine; 1.7% D6-DMSO; 50 mM sodium phosphate; 50 mM sodium Chloride; 0.02% sodium azide
Ionic strength: 50 mM NaCl and 50 mM sodium phosphate Not defined
Label: condition_1 / pH: 7.4 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
HADDOCKBonvinstructure calculation
XEASYBartels et al.peak picking
HADDOCKBonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 3
Details: 2MBT from the same group was used for HADDOCK model building
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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