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- PDB-7l7c: Crystal Structure of EcDsbA in a complex with 2-(6-(3-Methoxyphen... -

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Basic information

Entry
Database: PDB / ID: 7l7c
TitleCrystal Structure of EcDsbA in a complex with 2-(6-(3-Methoxyphenyl)benzofuran-3-yl)acetic acid
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 / Chem-XQ1 / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionDec 28, 2020Deposition 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 1.3Oct 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)42,6564
Polymers42,3102
Non-polymers3462
Water8,863492
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4372
Polymers21,1551
Non-polymers2821
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)117.317, 63.808, 74.073
Angle α, β, γ (deg.)90.000, 125.023, 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-307-

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) / Strain (production host): BL21(DE3) / References: UniProt: P0AEG4
#2: Chemical ChemComp-XQ1 / [6-(3-methoxyphenyl)-1-benzofuran-3-yl]acetic acid


Mass: 282.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O4 / 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.: 492 / 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: 54.16 %
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: Jun 17, 2014
RadiationMonochromator: DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→36.94 Å / Num. obs: 41619 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.042 / Rrim(I) all: 0.087 / Net I/σ(I): 13.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6027 / Rpim(I) all: 0.392 / Rrim(I) all: 0.807 / % possible all: 100

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Processing

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

1fvk


Resolution: 1.8→34.86 Å / SU ML: 0.1943 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1962 2090 5.02 %
Rwork0.1655 39524 -
obs0.1671 41614 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.94 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 22 492 3406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01553028
X-RAY DIFFRACTIONf_angle_d1.27054119
X-RAY DIFFRACTIONf_chiral_restr0.0766452
X-RAY DIFFRACTIONf_plane_restr0.0093562
X-RAY DIFFRACTIONf_dihedral_angle_d4.9836424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.30721320.27392607X-RAY DIFFRACTION100
1.84-1.890.29851300.25522618X-RAY DIFFRACTION100
1.89-1.940.25281300.22352629X-RAY DIFFRACTION99.93
1.94-20.24111310.19782628X-RAY DIFFRACTION100
2-2.060.23761420.18352638X-RAY DIFFRACTION99.96
2.06-2.130.1931580.17872613X-RAY DIFFRACTION100
2.13-2.220.21591290.17092622X-RAY DIFFRACTION100
2.22-2.320.23751350.17352614X-RAY DIFFRACTION100
2.32-2.440.19331430.16452647X-RAY DIFFRACTION100
2.44-2.60.21911380.16592620X-RAY DIFFRACTION100
2.6-2.80.18291370.16632648X-RAY DIFFRACTION100
2.8-3.080.20361460.15952624X-RAY DIFFRACTION99.96
3.08-3.520.18191630.15122646X-RAY DIFFRACTION100
3.52-4.440.15681290.13062659X-RAY DIFFRACTION100
4.44-34.860.16231470.15562711X-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)
10.557911087734-1.091529516790.04408418745042.06911854845-0.1834737724232.211222435210.04934109637250.3360621353440.272901245022-1.066210098220.0562520464514-0.329958534792-1.154891230321.081046097020.1001271540260.608197140869-0.208132623583-0.07838356937250.40040980114-0.01169961277450.051271091004230.2815736068-9.18386451177-11.5063962807
21.31071625919-0.0800758835484-0.2620231738712.304207273650.6591017663341.8392249595-0.01552234267040.01259566519830.0328105997371-0.103769672395-0.1483484262780.25069149267-0.0836621162065-0.2455656158760.1709498786330.130637201442-0.0225323143689-0.03213226368850.193392333325-0.03150611555840.11726064295828.0933311067-7.61912560518.5740506818
36.17119860562-2.50554089561-3.614549576633.227276285191.684393212464.34320769333-0.106450808584-0.258727790603-0.1032177764290.2435507603370.1209847295740.02507610344770.4773071830060.0291114953870.01136239320660.164890942654-0.0364560237815-0.06205174742580.198224704505-0.003792322905150.10935599441631.4366793507-19.31438093685.41849432222
40.6635054750481.086912359420.2403079550234.24405410122.361076634082.52699003916-0.095761200440.1208567155950.008014412812550.03296959354150.287333810303-0.6472538543860.004064543462890.138478129542-0.1292871268950.127563005335-0.0208299925215-0.004046126880060.1719042911360.006306699867780.11174765690836.2954588946-7.249178409874.19899322597
51.205140119190.134929894873-0.3298554938551.623565197170.05601268206931.399355290970.0253787943512-0.0367713075295-0.00471788963570.156337862902-0.0494300218902-0.004982139656880.0595331346519-0.03559367972440.02666361513010.142185206733-0.0325146210888-0.04360160006390.170047461817-0.004650111886660.082992322717933.9541685346-2.4671814245218.8842596459
60.5310871752440.797060122961-1.063043264463.72236963533-1.590010319553.065945236580.0799565118788-0.296276423062-0.08178409020420.331112030448-0.147175326001-0.7912959570490.0151201463790.6342909519690.01188379909470.206946501193-0.0202537284036-0.09955628192720.2807717664160.004966803177310.24353839760345.3790371251-0.62951498365822.7890086824
74.41142169591-0.9356345421972.37864447782.156318666170.4083005363094.85488987511-0.2693408884640.5006905656130.257953586803-1.008008367740.250281566649-0.433571945679-0.3855992940220.5321303269120.1481907002890.305248483114-0.07099921357510.01527585673090.1855411489540.04522949837860.19593921517342.43077262133.089458909414.98072220147
82.368535032850.316668673758-1.232535321661.27619019681.264050745183.9525667055-0.3645904884130.3362449528340.402387794521-1.112651960680.565174044459-0.114670556468-0.9292157032220.305041343370.2004406186890.452201729501-0.180454902558-0.05215314963170.293848197537-0.02660615780030.11124197488131.3123973514-6.01687636981-4.09578435512
92.421399767520.766135690185-0.6527678747242.579474231160.5376343261452.55864669071-0.0992749379890.219144390707-0.00975542524121-0.166506640595-0.0008812656780120.0882654474955-0.19104489959-0.009915334597370.09624518701050.158940439587-0.0326176164586-0.04356034813420.161588948526-0.02585434163030.088370333082825.3672629476-17.8614066836-3.44235363233
100.275473807094-0.00252713223726-0.251029847521.232303142341.28394000531.602653758130.2026856249840.1716413163560.112356622898-0.382679722150.1353803342970.207137673745-0.408305325444-0.130954943861-0.2489762799020.4025691001160.002478050696140.1094431454930.203107366744-0.03527539170740.344673046968.1708196799512.661250174525.6726589259
112.859795960460.5496036449392.21433350938.10344145461-2.282849059914.0676872657-0.346048544580.1337502930440.488732404875-0.5563262044740.2851888388440.401218684088-0.463650954722-0.7245492671810.09348107510840.4846071497340.158207306904-0.1064902035460.473750811558-0.05238667310940.621742742916-2.395419664095.1886876434914.8757045759
120.480315522999-0.02127423776510.000299970219620.5339911518060.6614376675951.25022397916-0.0369931720960.0672425767903-0.09557299444760.001413964467750.03742889549010.191543434129-0.0293659623184-0.01010949268640.01533508202580.222788518056-0.03223862374970.07958289286670.172645342484-0.02406271379950.34154480446910.4902820315-7.8024388886523.7106284382
131.11533842806-0.4068427591420.6324943612542.491201302891.17313566313.560476437410.254018446179-0.1805897552770.344263148956-0.0337984610391-0.2190970788290.542951630647-0.443128968254-0.347150563443-0.07584574244590.196244757046-0.02967162097110.03774688512450.227624223554-0.0295732291790.4014113041343.15683153027-6.5716787328518.5124080356
141.6805236933-0.29566271435-0.5694423198271.295223320.4530322293751.13490779679-0.0372907622192-0.00957826205287-0.1615796833220.0183087834169-0.01400403459190.208659039595-0.0173409749938-0.07031449013310.05693950521140.163618084203-0.04219250872680.02716233930380.178579684495-0.02012917870180.2636266608119.19820199306-20.756824272214.7905558909
153.256106204720.7050391907571.085325221341.88913611242-0.4388094737274.05819536435-0.1347695263690.25530245351-0.280958860049-0.2574348840260.09622346428770.173895407120.344904351373-0.2594628928120.026295203110.149157213648-0.04276608724590.00785313910230.221969418303-0.0575933209940.353572412896-0.680390039428-26.993067230411.6279406049
162.602121725020.194163566006-0.3881407535573.5027444716-0.05947472586513.62567531909-0.03677402786060.1463240228370.1520890826-0.35011156577-0.05873794695911.00475379357-0.556194486407-0.5986569574570.1381914354260.2644476259110.0762775947847-0.06373598959160.288373953320.02968147087990.429929071285-2.24093494731-8.684873126848.57159331612
175.63084637186-1.9866514752-0.6162962919045.009537833941.220929699444.71209458664-0.12983571960.2732410266280.522226861823-0.703973458470.133921490110.306571927862-0.447721835326-0.2450819104840.001526458881230.358060978050.007010214147230.01580051299150.2199608351630.03280630019330.3672167566195.319795473652.6073126655717.181072953
183.74984267121-0.468071579920.3238377936025.09734512542-1.968937037343.73897677943-0.202586206651-0.0377309305698-0.388789545318-0.5760774457630.150073805083-0.7096937527780.1425950518490.8161342847580.0373011383190.209679671538-0.03503970527930.1480201490270.267968889844-0.06084194883080.46741006474316.87202153845.2373480605927.4494333943
193.227642629220.4126748220310.9032512054882.843157687410.1178202863514.30222657011-0.09318708100180.02471181588460.267678673182-0.06372267191110.02735119583530.159299607958-0.0866293233036-0.2297354162820.05870636922940.20714587248-0.01110812527460.1282926356010.133863013379-0.02739226886320.3751634165637.075134503013.7340453676530.7435246644
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 21 )AA1 - 211 - 21
22chain 'A' and (resid 22 through 38 )AA22 - 3822 - 38
33chain 'A' and (resid 39 through 49 )AA39 - 4939 - 49
44chain 'A' and (resid 50 through 65 )AA50 - 6550 - 65
55chain 'A' and (resid 66 through 114 )AA66 - 11466 - 114
66chain 'A' and (resid 115 through 128 )AA115 - 128115 - 128
77chain 'A' and (resid 129 through 145 )AA129 - 145129 - 145
88chain 'A' and (resid 146 through 161 )AA146 - 161146 - 161
99chain 'A' and (resid 162 through 188 )AA162 - 188162 - 188
1010chain 'B' and (resid 1 through 11 )BC1 - 111 - 11
1111chain 'B' and (resid 12 through 21 )BC12 - 2112 - 21
1212chain 'B' and (resid 22 through 49 )BC22 - 4922 - 49
1313chain 'B' and (resid 50 through 65 )BC50 - 6550 - 65
1414chain 'B' and (resid 66 through 114 )BC66 - 11466 - 114
1515chain 'B' and (resid 115 through 128 )BC115 - 128115 - 128
1616chain 'B' and (resid 129 through 145 )BC129 - 145129 - 145
1717chain 'B' and (resid 146 through 161 )BC146 - 161146 - 161
1818chain 'B' and (resid 162 through 170 )BC162 - 170162 - 170
1919chain 'B' and (resid 171 through 188 )BC171 - 188171 - 188

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