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- PDB-6xsq: Crystal structure of E.coli DsbA in complex with 2-(6-(3-methoxyp... -

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Basic information

Entry
Database: PDB / ID: 6xsq
TitleCrystal structure of E.coli DsbA in complex with 2-(6-(3-methoxyphenyl)-2-(4-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-VE7 / 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 16, 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 1.3Oct 23, 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
Water2,864159
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)117.470, 63.640, 74.340
Angle α, β, γ (deg.)90.000, 125.290, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-370-

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-VE7 / [6-(3-methoxyphenyl)-2-(4-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.: 159 / 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: 2.68 Å3/Da / Density % sol: 54.11 %
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→31.82 Å / Num. obs: 20016 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.039 / Rrim(I) all: 0.079 / Net I/σ(I): 14.3 / Num. measured all: 80485 / Scaling rejects: 379
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
2.3-2.384.10.325801619670.910.1850.3754100
8.91-31.823.50.02412513550.9990.0140.02830.797

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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→31.82 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 1107 5.53 %
Rwork0.1904 18900 -
obs0.1931 20007 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.46 Å2 / Biso mean: 38.227 Å2 / Biso min: 18.53 Å2
Refinement stepCycle: final / Resolution: 2.3→31.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 49 159 3104
Biso mean--54.23 38.56 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012992
X-RAY DIFFRACTIONf_angle_d1.0274062
X-RAY DIFFRACTIONf_dihedral_angle_d12.551400
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: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.40.30251190.226423612480100
2.4-2.530.27921390.234123432482100
2.53-2.690.3121210.233823542475100
2.69-2.90.26671540.233223592513100
2.9-3.190.27351290.219323692498100
3.19-3.650.27691380.191223402478100
3.65-4.60.20611560.157323652521100
4.6-31.820.17181510.15442409256099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.59670.03911.44253.88552.39793.2056-0.04890.3095-0.1307-0.46680.06350.0547-0.13650.24770.01440.2276-0.0375-0.01060.2369-0.00490.199331.1504-9.7921.0171
21.79650.3850.73262.33781.02752.0929-0.04580.043-0.0013-0.10670.0396-0.0094-0.06120.10310.00710.1706-0.0302-0.02950.21150.01480.162133.83-5.66889.5861
32.08370.79580.79234.2862.04694.5766-0.00650.00560.4541-0.9789-0.23190.5003-0.9526-0.76820.33920.57080.17070.02740.37270.03380.54533.22349.564121.1957
40.75090.44491.19713.04932.29293.77240.1168-0.06550.17340.0807-0.12110.4313-0.1949-0.2953-0.06480.2367-0.01650.06990.2402-0.00670.38867.6109-7.452322.002
53.83420.3712-0.78374.62770.93733.88290.0586-0.0056-0.2191-0.1592-0.10380.084-0.16370.10940.04360.1883-0.04450.00340.2006-0.0170.25148.6687-20.729914.8312
65.40830.79730.75553.97691.45215.0134-0.15870.1106-0.4768-0.386-0.10520.38370.4989-0.50790.18120.2931-0.109-0.02290.3107-0.02260.3473-1.0456-27.412112.1028
73.82220.0163-1.00266.1698-0.17245.24210.13430.4990.496-0.7879-0.14541.305-0.6485-0.98970.01120.45370.1405-0.10420.42880.00680.4481-2.6883-8.79198.7036
83.43550.9504-0.55132.79391.2516.8006-0.01830.22190.422-0.99310.07690.1754-1.1609-0.67890.02830.58580.08860.06660.25960.03740.51524.47032.772317.192
90.72460.1492-0.59394.8404-4.14753.85840.147-0.20440.1716-0.2469-0.2857-0.6098-0.52411.322-0.02180.5214-0.10720.15990.3979-0.01570.482616.61355.224627.1393
103.89831.29860.61634.09310.7958.71940.2205-0.2260.5805-0.3624-0.36520.0862-0.1309-0.48880.0790.3696-0.04240.18310.1908-0.06930.49466.72753.687630.6326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 65 )A1 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 188 )A66 - 188
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 21 )B1 - 21
4X-RAY DIFFRACTION4chain 'B' and (resid 22 through 65 )B22 - 65
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 114 )B66 - 114
6X-RAY DIFFRACTION6chain 'B' and (resid 115 through 128 )B115 - 128
7X-RAY DIFFRACTION7chain 'B' and (resid 129 through 145 )B129 - 145
8X-RAY DIFFRACTION8chain 'B' and (resid 146 through 161 )B146 - 161
9X-RAY DIFFRACTION9chain 'B' and (resid 162 through 170 )B162 - 170
10X-RAY DIFFRACTION10chain 'B' and (resid 171 through 188 )B171 - 188

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