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- PDB-6xt3: Crystal structure of E.coli DsbA in complex with 3-(3-(carboxymet... -

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Basic information

Entry
Database: PDB / ID: 6xt3
TitleCrystal structure of E.coli DsbA in complex with 3-(3-(carboxymethyl)-6-(3-methoxyphenyl)benzofuran-2-yl)benzoic 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-VED / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 17, 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 6, 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)42,7764
Polymers42,3102
Non-polymers4662
Water4,324240
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5572
Polymers21,1551
Non-polymers4021
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)118.110, 63.360, 74.694
Angle α, β, γ (deg.)90.000, 125.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-384-

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-VED / 3-[3-(carboxymethyl)-6-(3-methoxyphenyl)-1-benzofuran-2-yl]benzoic acid


Mass: 402.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H18O6 / 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.: 240 / 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: 54.19 %
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: 1.99→37.28 Å / Num. obs: 31068 / % possible obs: 99.9 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.04 / Rrim(I) all: 0.082 / Net I/σ(I): 13.6 / Num. measured all: 128817 / Scaling rejects: 152
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
1.99-2.0440.891864921820.6220.511.031.299.7
9.1-37.283.60.02812323440.9980.0170.03344.698.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.99→34.74 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1589 5.12 %
Rwork0.2028 29470 -
obs0.2043 31059 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.22 Å2 / Biso mean: 46.8608 Å2 / Biso min: 19.46 Å2
Refinement stepCycle: final / Resolution: 1.99→34.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 47 240 3160
Biso mean--68.42 48.25 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022979
X-RAY DIFFRACTIONf_angle_d0.3644053
X-RAY DIFFRACTIONf_dihedral_angle_d10.595402
X-RAY DIFFRACTIONf_chiral_restr0.035445
X-RAY DIFFRACTIONf_plane_restr0.002531
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.99-2.050.32691190.321326502769
2.05-2.120.35981490.295826842833
2.12-2.210.28211640.270426282792
2.21-2.310.29491620.268926582820
2.31-2.430.28461630.229426382801
2.43-2.580.29391430.233927052848
2.58-2.780.23681140.220826872801
2.78-3.060.28341430.2126882831
3.06-3.50.21441680.191126602828
3.51-4.410.18611320.162527102842
4.42-34.740.17731320.173727622894
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)
11.0638-0.33621.34933.67641.95894.06320.11660.3119-0.1697-0.2435-0.00580.17140.04760.3993-0.05490.3217-0.0697-0.0330.33-0.07740.318431.1124-9.83091.1692
21.8466-0.29870.55472.29571.25933.4015-0.10290.1139-0.133-0.19580.02530.0932-0.0770.21780.05320.2019-0.03930.00330.2315-0.00940.210533.9521-5.66459.8064
30.6349-0.1034-0.38952.2051-0.961.5456-0.12860.17540.5911-0.6503-0.24910.4232-0.7155-0.33760.37740.5530.1063-0.0350.3536-0.05180.60162.9739.463221.4079
41.49340.28590.02881.15691.82793.69940.05040.0493-0.02420.1362-0.12270.30110.0398-0.17870.12720.3379-0.00360.10150.2441-0.01680.49619.8972-7.880123.5151
52.40850.02652.56526.3161.12924.2851-0.0036-0.12580.5317-0.4114-0.39880.7178-0.023-0.60250.21450.37720.0219-0.0050.3518-0.01540.45972.4853-7.065118.797
65.82260.9366-0.78385.04050.81593.7137-0.12370.25-0.5656-0.7352-0.007-0.614-0.04290.10050.13940.271-0.04940.08130.2449-0.01760.3478.3786-20.748814.8
78.67222.06432.55744.51870.23162.0058-0.65220.5493-0.7102-0.94650.1777-0.10410.6531-0.70440.33840.3805-0.11630.06210.4739-0.08860.261-1.4495-27.497312.294
82.31040.7316-0.14255.73760.95292.831-0.03130.21730.7997-1.0581-0.03930.5666-0.8554-0.65480.08490.50490.142-0.05280.47310.08830.46270.4701-3.30912.9963
96.2993-1.65590.70978.4671-5.49214.91070.2546-0.1373-0.0095-0.6933-0.3161-0.608-0.0720.97980.23630.5734-0.04240.21650.3206-0.02550.503316.33034.926927.1785
102.45442.22530.92493.43550.65645.64440.1179-0.25770.351-0.0411-0.26170.3862-0.28-0.51430.20680.43950.02850.18730.2423-0.09310.62056.5393.508130.7473
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 49 )B22 - 49
5X-RAY DIFFRACTION5chain 'B' and (resid 50 through 65 )B50 - 65
6X-RAY DIFFRACTION6chain 'B' and (resid 66 through 114 )B66 - 114
7X-RAY DIFFRACTION7chain 'B' and (resid 115 through 128 )B115 - 128
8X-RAY DIFFRACTION8chain 'B' and (resid 129 through 161 )B129 - 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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