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- PDB-8dg2: Crystal Structure of EcDsbA in a complex with DMSO -

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Basic information

Entry
Database: PDB / ID: 8dg2
TitleCrystal Structure of EcDsbA in a complex with DMSO
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / Microfrag screening
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 / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWhitehouse, R.L. / Ilyichova, O.V. / Taylor, A.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)IC180100021 Australia
Australian Research Council (ARC)DP200100796 Australia
CitationJournal: Rsc Med Chem / Year: 2023
Title: Fragment screening libraries for the identification of protein hot spots and their minimal binding pharmacophores.
Authors: Whitehouse, R.L. / Alwan, W.S. / Ilyichova, O.V. / Taylor, A.J. / Chandrashekaran, I.R. / Mohanty, B. / Doak, B.C. / Scanlon, M.J.
History
DepositionJun 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)43,56018
Polymers42,3102
Non-polymers1,25016
Water1,56787
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7949
Polymers21,1551
Non-polymers6398
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)21,7669
Polymers21,1551
Non-polymers6108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.246, 63.095, 74.547
Angle α, β, γ (deg.)90.000, 125.253, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 43 or resid 45...
d_2ens_1(chain "B" and (resid 2 through 3 or (resid 4...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNSERA1 - 42
d_12ens_1ASNGLUA44 - 84
d_13ens_1LYSVALA86 - 144
d_14ens_1LEUASNA146 - 169
d_15ens_1ASPLYSA171 - 187
d_16ens_1DMSDMSC
d_17ens_1DMSDMSD
d_18ens_1DMSDMSE
d_19ens_1DMSDMSF
d_110ens_1DMSDMSG
d_111ens_1DMSDMSH
d_112ens_1DMSDMSI
d_21ens_1GLNSERJ2 - 43
d_22ens_1ASNGLUJ45 - 85
d_23ens_1LYSVALJ87 - 145
d_24ens_1LEUASNJ147 - 170
d_25ens_1ASPLYSJ172 - 188
d_26ens_1DMSDMSL
d_27ens_1DMSDMSM
d_28ens_1DMSDMSN
d_29ens_1DMSDMSO
d_210ens_1DMSDMSP
d_211ens_1DMSDMSQ
d_212ens_1DMSDMSR

NCS oper: (Code: givenMatrix: (-0.960656804927, 0.0579811227938, 0.271618652797), (-0.272471823624, -0.00720250017734, -0.96213680385), (-0.0538294387736, -0.998291697547, 0.0227173530712)Vector: 35. ...NCS oper: (Code: given
Matrix: (-0.960656804927, 0.0579811227938, 0.271618652797), (-0.272471823624, -0.00720250017734, -0.96213680385), (-0.0538294387736, -0.998291697547, 0.0227173530712)
Vector: 35.3708186378, 8.62043259307, 14.8858287809)

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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 K-12 (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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.78 %
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: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.95→48.11 Å / Num. obs: 32516 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 33.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.056 / Rrim(I) all: 0.107 / Χ2: 0.998 / Net I/σ(I): 9.4
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.155 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2243 / CC1/2: 0.763 / Rpim(I) all: 0.727 / Χ2: 0.81 / % possible all: 100

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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: 1.95→47.87 Å / SU ML: 0.1954 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5711
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2216 1728 5.32 %
Rwork0.1887 30753 -
obs0.1904 32481 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2847 0 63 87 2997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792991
X-RAY DIFFRACTIONf_angle_d0.90834062
X-RAY DIFFRACTIONf_chiral_restr0.0518447
X-RAY DIFFRACTIONf_plane_restr0.0065532
X-RAY DIFFRACTIONf_dihedral_angle_d4.5939405
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.84627191748 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.28721350.25342523X-RAY DIFFRACTION99.66
2.01-2.070.261450.23472550X-RAY DIFFRACTION99.93
2.07-2.150.26831400.2212556X-RAY DIFFRACTION99.93
2.15-2.230.22781470.20932548X-RAY DIFFRACTION99.93
2.23-2.330.25531510.19182542X-RAY DIFFRACTION100
2.33-2.460.24091690.19242522X-RAY DIFFRACTION99.85
2.46-2.610.20611340.19012579X-RAY DIFFRACTION99.93
2.61-2.810.23911370.19772550X-RAY DIFFRACTION100
2.81-3.10.23351450.18932565X-RAY DIFFRACTION99.93
3.1-3.540.2241590.1822569X-RAY DIFFRACTION100
3.54-4.460.19631370.16182601X-RAY DIFFRACTION99.89
4.46-47.870.20391290.19262648X-RAY DIFFRACTION99.82
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)
13.06885691381.54330547205-0.7385306342595.26264441799-0.8143619769811.33355276299-0.4281121814920.270961001552-0.506112683998-1.664633064130.2718090502150.0187948713942-0.06850678550160.0169053612760.2544367481720.80751951509-0.0537039929952-0.0367313583640.626414291055-0.03928225504990.42393294269230.5398981932-7.74623467016-10.4514364659
21.505974989741.019907741861.080875822082.201820205960.7200981463132.21355367595-0.006395548128880.0918387786055-0.299957015792-0.0240589897952-0.03286851627050.0470195961957-0.02160788503840.1532476228240.07203389181620.294395249452-0.05943057923620.01030745436460.287577097549-0.0143557139710.32999304880430.7064322711-8.763131702356.3537924937
32.528689777380.7929754992790.2888390140991.787511886310.5429376150743.36675632619-0.150922314294-0.1481607090970.083377834377-0.02498325104620.07797449277310.0277130262258-0.0695648723830.1881228268950.07590821939660.239521102739-0.0461472991372-0.01940828118080.269734374374-0.01253449931820.22371968804335.8028733722-1.7799616236120.0269163676
43.402029039490.3602603072533.21697836570.8289640522370.5155427074033.078236676780.09755727277260.2610986916050.113076341406-0.4273545556070.0665347793196-0.127147465844-0.2767063031730.752170342132-0.1698042000810.372910299842-0.1692624762440.03645338412340.420155191488-0.02249913865360.29881680687142.53105755824.24100523985.98604583258
52.41362015973-0.292280654906-0.3147764513612.323342399440.05632217455391.712920962010.02475286148780.630715761725-0.133286358697-1.36559930728-0.2156425045770.520515335605-0.692916497499-0.06664907100910.2092826108640.576463559524-0.0987965350266-0.04836656887680.425542001369-0.02319551854270.30345660254630.9126330531-3.49491693987-4.1722753171
62.894697122281.20926926376-0.5913802794272.56813854838-0.4011301375712.59377377692-0.0727234923074-0.03282968268320.264594673853-0.2737913855050.05627732062040.530968551877-0.0722272277734-0.1749210980930.1067403224910.3961962161040.0188706328158-0.0540890979380.345794831794-0.106336668040.42491909760124.5105168439-16.2892657686-2.79763916576
72.387501144130.1362465522020.2732018162770.368456851443-0.07463702008653.396323083960.119615899566-0.1767062053810.805735714895-0.189738094184-0.06262131310480.423243916325-0.838841957682-0.544069923308-0.1209046311960.4827423999290.1008441926220.01423995801630.3364769847670.04724204455170.5021343106143.0187238881710.894948543821.6926052969
82.076247318070.1665021302140.4159889070720.865248716730.03506840901351.05756229082-0.193925976534-0.1134671411780.07372337067650.007592032030520.1857747885450.03303138737110.0544493691719-0.1265921413050.0207342725930.261049830588-0.04101728740570.01752693097730.273264850668-0.01714366520030.3420922610611.0447380101-7.1720326409319.6764341536
96.73930064421-1.72526323312-1.234927805133.934651485320.4570374872643.799113082770.171584565607-0.29342281634-0.2033485910380.5794054162060.0765525531221.139409400850.00481628882962-0.116419549383-0.286443298390.357229741574-0.008925546529520.08768710154670.314804181488-0.0417070993530.4671476922227.4689843644-4.6181534424531.1998770686
101.02728730804-1.01448226340.5433479252453.655766011781.002399928712.933891047760.443279306202-0.2695920460990.959658495728-0.2046199540080.04823814048650.176273333028-0.0702805663331-0.179430619234-0.2875815708850.288198151665-0.1014126865420.02142219201080.440922357585-0.03220365968590.5063101319152.38976140756-4.9809957299718.5208535853
112.255885921260.412793551394-0.6789641296212.892792137950.2245129972351.40449436728-0.06022989556650.0887029287955-0.2810001369230.0182317323116-0.13785861969-0.1058454514990.261435778148-0.2166643286110.1744411247810.261485167399-0.07118871842740.01028207556680.31016699126-0.01934387810840.2688517749776.0105396695-20.65209274714.3051153093
121.893465632610.665169708294-0.9027547543254.71324914669-0.3287098571882.30304337366-0.05327469819320.2712941274370.443660067683-0.616081889592-0.3823717476540.433804088914-0.466232019-0.6343049166410.4262985580850.3992059149930.0781091749092-0.1493657708260.505788238040.01916505694850.410759474996-3.47570255901-8.056497987018.86106780788
132.73365300743-1.0762001460.8391667997463.233944537620.2967163385192.07452756851-0.005339510573570.004843060910520.0331925889257-0.719171801746-0.03122938624750.472879970402-0.629055599175-0.4535245324530.04566379985610.4737857019230.0792173403609-0.01584468130830.319627685139-0.01097081701140.4770276480944.757716600014.021436792316.4526890996
143.623784102280.3128919446640.08278923439572.993569654220.4731548711473.20309366695-0.0801717617284-0.5113474233130.454066831274-0.05125830398540.1125760273120.00166142418222-0.1902130943950.0969650591201-0.0655480484180.3934538850090.006761126307710.1111806020690.279011526763-0.06345754016330.4459919891559.669818234215.3967976211429.8921188007
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 21 )AA2 - 211 - 20
22chain 'A' and (resid 22 through 65 )AA22 - 6521 - 64
33chain 'A' and (resid 66 through 128 )AA66 - 12865 - 127
44chain 'A' and (resid 129 through 144 )AA129 - 144128 - 143
55chain 'A' and (resid 145 through 161 )AA145 - 161144 - 160
66chain 'A' and (resid 162 through 188 )AA162 - 188161 - 187
77chain 'B' and (resid 1 through 21 )BJ1 - 211 - 21
88chain 'B' and (resid 22 through 38 )BJ22 - 3822 - 38
99chain 'B' and (resid 39 through 49 )BJ39 - 4939 - 49
1010chain 'B' and (resid 50 through 65 )BJ50 - 6550 - 65
1111chain 'B' and (resid 66 through 128 )BJ66 - 12866 - 128
1212chain 'B' and (resid 129 through 144 )BJ129 - 144129 - 144
1313chain 'B' and (resid 145 through 161 )BJ145 - 161145 - 161
1414chain 'B' and (resid 162 through 188 )BJ162 - 188162 - 188

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