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- PDB-7lhp: Crystal Structure of EcDsbA in a complex with methyl 2-(6-bromo-2... -

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Basic information

Entry
Database: PDB / ID: 7lhp
TitleCrystal Structure of EcDsbA in a complex with methyl 2-(6-bromo-2-phenylbenzofuran-3-yl)acetate
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / OXIDOREDUCTASE-INHIBITOR COMPLEX / OXIDOREDUCTASE
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 / (6-bromo-2-phenyl-1-benzofuran-3-yl)acetic acid / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsIlyichova, O.V. / Scanlon, M.J.
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
DepositionJan 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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)42,7054
Polymers42,3102
Non-polymers3952
Water7,134396
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4862
Polymers21,1551
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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
MethodPISA
Unit cell
Length a, b, c (Å)118.211, 63.803, 74.767
Angle α, β, γ (deg.)90.000, 125.705, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-455-

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 / Plasmid: B0013 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEG4
#2: Chemical ChemComp-Y1G / (6-bromo-2-phenyl-1-benzofuran-3-yl)acetic acid


Mass: 331.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11BrO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 11-13 % PEG 8000, 5-7.5% glycerol, 100mM Na Cacodylate pH6.1, 1mM CuCl2

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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: Mar 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→48.5 Å / Num. obs: 35727 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 27.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.038 / Rrim(I) all: 0.078 / Net I/σ(I): 14
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.871 / Num. unique obs: 5181 / CC1/2: 0.678 / Rpim(I) all: 0.484 / Rrim(I) all: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.9→37.32 Å / SU ML: 0.2376 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8212
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2254 1725 4.83 %
Rwork0.1794 33997 -
obs0.1815 35722 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.53 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 21 396 3287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662988
X-RAY DIFFRACTIONf_angle_d0.86644066
X-RAY DIFFRACTIONf_chiral_restr0.0496449
X-RAY DIFFRACTIONf_plane_restr0.0057554
X-RAY DIFFRACTIONf_dihedral_angle_d4.7593419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.32231390.29882800X-RAY DIFFRACTION100
1.96-2.020.28491300.25432816X-RAY DIFFRACTION100
2.02-2.090.26221360.23372835X-RAY DIFFRACTION99.97
2.09-2.170.28861300.22132838X-RAY DIFFRACTION100
2.17-2.270.27841450.21292822X-RAY DIFFRACTION100
2.27-2.390.24981840.19282780X-RAY DIFFRACTION99.97
2.39-2.540.23531430.18582804X-RAY DIFFRACTION100
2.54-2.740.24591520.17982837X-RAY DIFFRACTION100
2.74-3.020.22661580.18412827X-RAY DIFFRACTION100
3.02-3.450.20661470.16892817X-RAY DIFFRACTION100
3.45-4.350.20591380.14642868X-RAY DIFFRACTION100
4.35-37.320.17861230.15722953X-RAY DIFFRACTION99.97
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)
10.466552673712-0.444222226260.7231948547963.982334601851.918210541492.832268621450.09832376018950.220348476606-0.0748615752679-0.319599840583-0.0988890825050.0984914016167-0.08999767453630.340103511371-0.01045358103050.195705714692-0.0441572334997-0.02029572034910.312567457219-0.0379541883760.17777019664631.0608552372-8.898551214931.34593127715
21.21110078932-0.4602376570260.4030649253662.496399205781.060487970432.67998644163-0.0888932360590.214900366626-0.0843979115319-0.107345330355-0.02093593006130.0873765883332-0.06386495195040.2539805183980.07098787598040.153173166479-0.055249481817-0.02086584410410.236515058287-0.01299734589110.13720166419533.6772634844-4.674644291889.33017792922
33.369076552760.266822719166-3.241363048833.062135312141.351448990963.963832252220.5411233035790.2508646641180.666790600737-0.801299838262-0.08757354290470.109551642217-1.34303940555-0.174114286027-0.3727841418450.5653288080650.09339548880540.1129056741440.2709828414610.01865209353450.3703645406617.4799856880213.796853608725.7748099088
41.208000148740.3665141472621.899674671748.15787298884-2.481525061064.149343502770.07610921390980.3380029930690.634370786233-0.666396560110.2781526605091.33742000566-0.257693708365-1.18437065368-0.3841164693410.5078852818690.196225055941-0.09101877592090.7596793103060.001577279341030.720319728271-3.68251669335.8962208371715.1867341904
51.284106561631.15399731299-0.4708089678992.306805873212.103853960785.104501090560.1363601183650.08517020095260.07266317621030.125054758973-0.06900040758750.353299964102-0.0265499041979-0.247677372736-0.07194132025440.217090178670.008059948401480.06758391156720.1598481043850.02081098278090.3020314714259.93059672103-6.6141836164223.5295574217
62.62441000008-0.8850554861510.8088286107067.084539742351.766869283633.966492899630.120988109734-0.2031039947320.410108008288-0.525721376122-0.2582051641790.754097710838-0.407911246309-0.5341600902850.1710981287980.2274077792740.0168892794929-0.06796060363110.4445024314330.02827413937180.4106403431382.4370183732-5.5608218724318.5737439901
74.575559574810.593190938522-1.886445998725.718870361671.34850379414.14782977405-0.08224730946840.113247718562-0.222783218498-0.230538344578-0.1643164737-0.02239001324410.0939853562758-0.2543978914910.227287938610.155265361576-0.021349831307-0.01218944848880.2066408970190.002469480434160.1941415840478.48818753989-19.602938059214.8355767111
87.016338302580.9001340267581.985038455854.59390889233-1.416644993945.7047013586-0.3019554033890.305581401249-0.517999370126-0.7350329988230.07793206624910.352912218050.612806431807-0.7324716258550.1502583620160.265578746912-0.109043038053-0.02759839874120.371956478675-0.07963780664830.266119767383-1.32150321457-26.286216070312.0859526683
92.91855614626-0.2640358716450.4205283535931.918569085460.6843508737782.086940838240.2098378538780.3287201412940.63124679397-0.810121994764-0.02229818773690.505725489464-0.710519460419-0.70736751091-0.01179649319010.4655767709950.178239254429-0.0359026725010.4525814169710.128597229920.4087879057280.773315101689-2.0325312994313.1112390795
101.959286852521.93970852192-2.69217373345.93215600824-4.990837376835.3280948849-0.0679233374796-0.1615384362160.0847123025942-0.553920408335-0.295300435615-0.888376894274-0.5089654433551.157328389210.4149138929840.450256784084-0.06406931572280.1909014936190.32601239534-0.003318798595970.50937675368316.36710392756.3753197648227.5129390553
112.06546077495-0.3403885218441.150335260513.462200248180.9491460594445.966771393270.0531886093143-0.09429278579760.4464102659770.246231172039-0.1826185095130.365619744787-0.340772834688-0.5155607501010.1787802559830.3711584390590.05791126134530.1939793930640.199574157384-0.01201208736340.4853148399446.453443558554.8444224696430.6813328565
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 65 )AA1 - 651 - 65
22chain 'A' and (resid 66 through 188 )AA66 - 18866 - 188
33chain 'B' and (resid 1 through 11 )BC1 - 111 - 11
44chain 'B' and (resid 12 through 21 )BC12 - 2112 - 21
55chain 'B' and (resid 22 through 49 )BC22 - 4922 - 49
66chain 'B' and (resid 50 through 65 )BC50 - 6550 - 65
77chain 'B' and (resid 66 through 114 )BC66 - 11466 - 114
88chain 'B' and (resid 115 through 128 )BC115 - 128115 - 128
99chain 'B' and (resid 129 through 161 )BC129 - 161129 - 161
1010chain 'B' and (resid 162 through 170 )BC162 - 170162 - 170
1111chain 'B' and (resid 171 through 188 )BC171 - 188171 - 188

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