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- PDB-6xsp: Crystal structure of E.coli DsbA in complex with 2-(2,6-bis(3-met... -

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Basic information

Entry
Database: PDB / ID: 6xsp
TitleCrystal structure of E.coli DsbA in complex with 2-(2,6-bis(3-methoxyphenyl)benzofuran-3-yl)acetic acid
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/INHIBITOR / Inhibitor / complex / disulfide oxidoreductase / fragments / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
COPPER (II) ION / Chem-VCY / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, G. / Heras, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1099151 Australia
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: Elaboration of a benzofuran scaffold and evaluation of binding affinity and inhibition of Escherichia coli DsbA: A fragment-based drug design approach to novel antivirulence compounds.
Authors: Duncan, L.F. / Wang, G. / Ilyichova, O.V. / Dhouib, R. / Totsika, M. / Scanlon, M.J. / Heras, B. / Abbott, B.M.
History
DepositionJul 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7624
Polymers42,3102
Non-polymers4522
Water3,693205
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5432
Polymers21,1551
Non-polymers3881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2192
Polymers21,1551
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.080, 63.820, 74.370
Angle α, β, γ (deg.)90.000, 125.730, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-383-

HOH

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21155.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEG4
#2: Chemical ChemComp-VCY / [2,6-bis(3-methoxyphenyl)-1-benzofuran-3-yl]acetic acid


Mass: 388.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 11-13% PEG 8000, 5-7.5% glycerol, 1 mM copper(II) chloride, 100 mM sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→31.91 Å / Num. obs: 19927 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.035 / Rrim(I) all: 0.072 / Net I/σ(I): 13.8 / Num. measured all: 80257 / Scaling rejects: 331
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3840.273800219770.9260.1540.3144.6100
8.91-31.913.50.0312273540.9950.0190.03627.897

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 2.3→31.91 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 1040 5.22 %
Rwork0.1918 18883 -
obs0.1946 19923 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.23 Å2 / Biso mean: 34.8949 Å2 / Biso min: 11.69 Å2
Refinement stepCycle: final / Resolution: 2.3→31.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 49 205 3152
Biso mean--59.79 33.95 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092994
X-RAY DIFFRACTIONf_angle_d0.9564064
X-RAY DIFFRACTIONf_dihedral_angle_d11.519401
X-RAY DIFFRACTIONf_chiral_restr0.052444
X-RAY DIFFRACTIONf_plane_restr0.006529
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.420.35281410.258526822823
2.42-2.570.3041530.248226822835
2.57-2.770.32851460.244526812827
2.77-3.050.32281530.230826832836
3.05-3.490.25191560.195326842840
3.49-4.40.21571550.15426982853
4.4-31.910.15921360.154127732909

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