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- PDB-5dch: Crystal structure of Pseudomonas aeruginosa DsbA E82I in complex ... -

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Basic information

Entry
Database: PDB / ID: 5dch
TitleCrystal structure of Pseudomonas aeruginosa DsbA E82I in complex with MIPS-0000851 (3-[(2-METHYLBENZYL)SULFANYL]-4H-1,2,4-TRIAZOL-4-AMINE)
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / thioredoxin fold
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.447 Å
AuthorsMcMahon, R.M. / Martin, J.L.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)LP0990166 Australia
Australian Research Council (ARC)FL0992138 Australia
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 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)22,1357
Polymers21,3521
Non-polymers7846
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.470, 63.100, 41.870
Angle α, β, γ (deg.)90.000, 98.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21351.514 Da / Num. of mol.: 1 / Mutation: E82I
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 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / 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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20-29 % PEG 1500, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.447→35.1 Å / Num. obs: 31349 / % possible obs: 96.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 15.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.032 / Net I/σ(I): 14.1 / Num. measured all: 232922 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.447-1.477.11.0812.31023414510.8080.43592.1
7.93-35.15.90.0433.312432090.9950.01996.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.1.27data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H93

3h93


Resolution: 1.447→35.098 Å / FOM work R set: 0.9076 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1632 1574 5.03 %
Rwork0.1359 29729 -
obs0.1373 31303 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.58 Å2 / Biso mean: 19.19 Å2 / Biso min: 6.87 Å2
Refinement stepCycle: final / Resolution: 1.447→35.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 96 141 1704
Biso mean--35.81 32.49 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081620
X-RAY DIFFRACTIONf_angle_d1.1482203
X-RAY DIFFRACTIONf_chiral_restr0.064233
X-RAY DIFFRACTIONf_plane_restr0.006278
X-RAY DIFFRACTIONf_dihedral_angle_d12.829616
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4471-1.49380.24021320.19482607273993
1.4938-1.54720.2351330.16692667280095
1.5472-1.60910.19431240.1382688281295
1.6091-1.68230.17041600.12582671283196
1.6823-1.7710.16721570.12052628278595
1.771-1.8820.17361400.11332723286397
1.882-2.02730.14011380.11222715285397
2.0273-2.23130.14831590.11142718287797
2.2313-2.55410.15791310.11722759289097
2.5541-3.21750.16271510.14042740289197
3.2175-35.10790.15771490.15632813296298

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