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- PDB-6pvy: E.coli DsbA in complex with benzofuran compound 26 ([6-(3-methoxy... -

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Basic information

Entry
Database: PDB / ID: 6pvy
TitleE.coli DsbA in complex with benzofuran compound 26 ([6-(3-methoxyphenoxy)-1-benzofuran-3-yl]acetic acid)
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibitor / complex / disulfide oxidoreductase / fragments / 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 / 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
COPPER (II) ION / Chem-OZG / DI(HYDROXYETHYL)ETHER / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsWang, G. / Heras, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1099151 Australia
CitationJournal: Molecules / Year: 2019
Title: The Fragment-Based Development of a Benzofuran Hit as a New Class of Escherichia coli DsbA Inhibitors.
Authors: Duncan, L.F. / Wang, G. / Ilyichova, O.V. / Scanlon, M.J. / Heras, B. / Abbott, B.M.
History
DepositionJul 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)42,9347
Polymers42,3102
Non-polymers6245
Water4,756264
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6384
Polymers21,1551
Non-polymers4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2973
Polymers21,1551
Non-polymers1422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.317, 63.895, 74.461
Angle α, β, γ (deg.)90.000, 125.840, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 269 molecules

#2: Chemical ChemComp-OZG / [6-(3-methoxyphenoxy)-1-benzofuran-3-yl]acetic acid


Mass: 298.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cu
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 11-13% PEG8000, 5-7.5% glycerol, 1 mM copper(II) chloride, 100 mM sodium cacodylate
PH range: 6.0-6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95366 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 23, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 1.74→48.45 Å / Num. obs: 45582 / % possible obs: 98.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.17 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.043 / Rrim(I) all: 0.084 / Net I/σ(I): 6.6 / Num. measured all: 161630 / Scaling rejects: 20
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
1.74-1.773.20.538739122940.8280.3480.6431.491.7
9.02-48.453.40.06210433070.9790.0390.07410.386.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
iMOSFLM7.2.2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FVK

1fvk


Resolution: 1.74→34.63 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.33
RfactorNum. reflection% reflection
Rfree0.2253 2417 5.31 %
Rwork0.1925 --
obs0.1943 45558 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.67 Å2 / Biso mean: 47.3 Å2 / Biso min: 22.97 Å2
Refinement stepCycle: final / Resolution: 1.74→34.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 68 264 3205
Biso mean--92.48 49.43 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042973
X-RAY DIFFRACTIONf_angle_d0.6124037
X-RAY DIFFRACTIONf_chiral_restr0.041444
X-RAY DIFFRACTIONf_plane_restr0.004525
X-RAY DIFFRACTIONf_dihedral_angle_d9.8521742
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7365-1.77190.35111160.31092373248993
1.7719-1.81040.30731340.27152562269699
1.8104-1.85250.30561490.25912538268799
1.8525-1.89890.29141270.25032538266599
1.8989-1.95020.26811320.24012569270199
1.9502-2.00760.21021140.23252569268399
2.0076-2.07240.28021450.22962520266599
2.0724-2.14640.2331550.220525442699100
2.1464-2.23240.26571700.221125322702100
2.2324-2.33390.26051480.218425592707100
2.3339-2.4570.23241460.21432542268899
2.457-2.61080.25611290.22082562269199
2.6108-2.81230.25731720.20942521269399
2.8123-3.09520.25121260.20592558268499
3.0952-3.54270.23361600.18542543270399
3.5427-4.46190.18551420.1512543268598
4.4619-34.63670.18051520.16672568272097
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)
1-0.0423-0.58291.33625.85864.02374.97870.00380.3026-0.0261-0.15450.03540.0342-0.05650.2996-0.02510.267-0.0936-0.00580.3849-0.05820.295330.7373-9.69780.9308
23.21681.10040.01252.53230.14024.954-0.17130.11140.0177-0.00970.0855-0.12450.06390.32620.080.2037-0.0183-0.02390.2178-0.01320.235536.9356-1.42616.962
32.0651.0197-0.03443.12851.63684.82690.01760.29770.0308-0.53840.030.5277-0.1260.378-0.03740.3377-0.0055-0.06310.4268-0.0830.35927.38-13.3044-3.9271
40.8190.4965-0.4964.43342.79263.70290.31050.18540.432-0.5064-0.29640.4057-0.6496-0.6911-0.02670.37440.08690.05440.363-0.00070.45345.6133-2.320121.5995
53.2016-0.279-3.13626.80951.94215.15380.0211-0.0674-0.4552-0.2387-0.1229-0.085-0.0211-0.00440.12850.2297-0.0352-0.02040.27460.00220.28018.3416-20.883815.037
65.95812.07770.49962.24881.5912.1129-0.43230.3803-0.7361-0.5432-0.14780.34960.3392-0.64120.54040.3285-0.07320.00620.4738-0.02770.3779-1.3995-27.682612.0695
72.12491.1135-2.38529.2328-3.53583.22220.01811.00930.2362-1.41790.21540.5957-0.7069-1.103-0.14650.60770.2372-0.16090.65920.10810.4696-3.9617-10.05648.3642
86.12660.62262.08894.7303-0.33492.07780.4134-0.10881.3596-1.1324-0.08580.3281-1.5574-0.6723-0.23720.80810.21320.10150.45120.05290.6443.93642.35216.9027
94.20982.47292.36675.9389-1.39353.34270.14910.00180.5237-0.4001-0.2566-0.1182-0.23360.01340.1080.50590.06140.17920.2976-0.04580.53259.15284.152129.3427
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 144 )A66 - 144
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 188 )A145 - 188
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 65 )B1 - 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 144 )B129 - 144
8X-RAY DIFFRACTION8chain 'B' and (resid 145 through 161 )B145 - 161
9X-RAY DIFFRACTION9chain 'B' and (resid 162 through 188 )B162 - 188

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