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- PDB-8dg1: Crystal Structure of EcDsbA in a complex with DMSO -

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Basic information

Entry
Database: PDB / ID: 8dg1
TitleCrystal Structure of EcDsbA in a complex with DMSO
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / Microfrag screening / FBDD / Fragment / ANTIMICROBIAL PROTEIN
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)43,93623
Polymers42,3102
Non-polymers1,62621
Water1,44180
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,01412
Polymers21,1551
Non-polymers85911
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)21,92211
Polymers21,1551
Non-polymers76710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.214, 63.205, 74.848
Angle α, β, γ (deg.)90.000, 125.254, 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 34 or resid 36...
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_1GLNTYRA1 - 33
d_12ens_1PHESERA35 - 42
d_13ens_1ASNLYSA44 - 54
d_14ens_1THRGLNA56 - 137
d_15ens_1LYSLYSA139 - 187
d_16ens_1DMSDMSC
d_17ens_1DMSDMSD
d_18ens_1DMSDMSE
d_21ens_1GLNTYRL2 - 34
d_22ens_1PHESERL36 - 43
d_23ens_1ASNLYSL45 - 55
d_24ens_1THRGLNL57 - 138
d_25ens_1LYSLYSL140 - 188
d_26ens_1DMSDMSN
d_27ens_1DMSDMSO
d_28ens_1DMSDMSP

NCS oper: (Code: givenMatrix: (-0.958315526405, 0.0573409900717, 0.279898843706), (-0.279738116507, 0.0109750370984, -0.960013611744), (-0.0581200311732, -0.998294325046, 0.00552291210703)Vector: 35. ...NCS oper: (Code: given
Matrix: (-0.958315526405, 0.0573409900717, 0.279898843706), (-0.279738116507, 0.0109750370984, -0.960013611744), (-0.0581200311732, -0.998294325046, 0.00552291210703)
Vector: 35.1702959263, 9.06895316011, 15.1681004274)

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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-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


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


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
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→48.23 Å / Num. obs: 32730 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 37.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Χ2: 0.95 / Net I/σ(I): 15.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.183 / Mean I/σ(I) obs: 2 / Num. unique obs: 2296 / CC1/2: 0.727 / Rpim(I) all: 0.693 / Χ2: 0.95 / % 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→47.86 Å / SU ML: 0.2067 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7798
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2213 1739 5.31 %
Rwork0.1898 30980 -
obs0.1914 32719 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.15 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 81 80 3007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793008
X-RAY DIFFRACTIONf_angle_d0.90124078
X-RAY DIFFRACTIONf_chiral_restr0.0543447
X-RAY DIFFRACTIONf_plane_restr0.0068531
X-RAY DIFFRACTIONf_dihedral_angle_d4.5321401
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.13923742397 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.30891370.26142575X-RAY DIFFRACTION99.93
2.01-2.070.26341450.23372565X-RAY DIFFRACTION100
2.07-2.150.26381410.21662580X-RAY DIFFRACTION100
2.15-2.230.25771510.21262561X-RAY DIFFRACTION99.93
2.23-2.330.26211500.20012551X-RAY DIFFRACTION100
2.33-2.460.24381730.19332539X-RAY DIFFRACTION100
2.46-2.610.21521310.19342574X-RAY DIFFRACTION100
2.61-2.810.22391380.19832589X-RAY DIFFRACTION100
2.81-3.090.22791440.18712581X-RAY DIFFRACTION99.96
3.1-3.540.22911610.18192582X-RAY DIFFRACTION100
3.54-4.460.19531380.16642619X-RAY DIFFRACTION100
4.46-47.860.20161300.19322664X-RAY DIFFRACTION99.89
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)
16.636082197791.0997306312-1.170025827887.42947895298-2.802118606165.28845677079-0.3949749184750.967661978515-0.739030269492-1.675582370640.6173361099640.35514538273-0.0701616657-0.0682050505655-0.1999476748150.817032541968-0.0442412006335-0.07776967191320.545192331494-0.1312390462790.48224210562830.5845317499-7.72296401295-10.5592203646
22.325281845671.541261279270.8322534256273.189346922730.712069833383.032201977160.02127587037350.0794795080568-0.2409970958060.0263340696034-0.04312180661020.01916619682670.0850587297240.1823534636250.03515991144070.292115048549-0.0600664007868-0.002770616110110.288616422909-0.02356639676240.28993926163530.5942571092-8.823137690356.36630199192
32.833505707660.644486386697-0.3800954529412.20395934059-0.1462351204754.01690604928-0.0940227091945-0.06330767939680.0345635322481-0.1354032304850.076374282499-0.0373423778437-0.08567440161490.2953444302240.01160277962550.237578670665-0.0625378101908-0.01546287087020.235542287223-0.02889603783010.22976403974837.0673166192-0.28636642616917.0946344719
41.342424170380.6813878138430.6483737020346.048623106121.326705507052.435024738380.01841652549270.227996572378-0.126144809566-0.795800176571-0.1544442288050.673427247151-0.0955700178342-0.07457640294340.123203602550.437469632235-0.00915919981157-0.08222397506810.372487936113-0.0683080713850.33135176063427.0562128671-11.6801271092-3.58527492717
52.117011833090.338277929722-0.2519519886151.657617839291.331368153893.29525390353-0.04904441770670.01789837356860.267028215914-0.05327247774540.04944712811550.3977560481-0.271470664535-0.2241768179910.0007662607116120.296234907375-0.01266980070260.04383736197560.259504407247-0.001759167683360.4016218424386.960842217760.38467935111123.1120542186
62.53353381053-1.72838921591-0.9082361219335.375693098633.336013191765.977331205660.462677333637-0.4591554425090.915550900487-0.20286022333-0.03672565033340.246163201765-0.13543099762-0.0559085682319-0.3192063973820.337537648937-0.1251963965570.001039139393690.470771246927-0.04193405518740.556433324222.35986911523-5.0993728418918.7462183185
73.575378069460.353358284359-1.245520968053.438261133190.3144009995282.77996817468-0.06418505089450.118688421236-0.3108346215310.0274107683475-0.132085237963-0.1282364936260.352256930307-0.2395039743560.1760158666590.248057085626-0.0722860759680.007561200773010.262889931172-0.01195620820940.2438617373195.96697233889-20.658213868714.3601382799
84.265980389553.12721921891-1.425884277946.64269209823-1.149155760495.16957323611-0.1377445388010.5929623956150.592404719015-0.690151171061-0.06978586742990.646171553756-0.50843507293-0.7742056646690.2355289140590.4231924932060.0658090126409-0.1382874995330.5090991675670.02790410842630.417832819132-3.46494483281-8.27151472258.96496545333
91.891365111321.186137666620.6955187317912.447020348490.9433899784616.331332017230.0889823293271-0.1337840682140.336969985257-0.109083183327-0.06477354843540.333937278126-0.394754464407-0.243427795258-0.01439701920550.3638425009470.0406693969280.06892001753650.219068125376-0.03008087805570.460941998927.573804810725.0240880459925.4286336565
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 144 )AA66 - 14465 - 143
44chain 'A' and (resid 145 through 188 )AA145 - 188144 - 187
55chain 'B' and (resid 1 through 49 )BL1 - 491 - 49
66chain 'B' and (resid 50 through 65 )BL50 - 6550 - 65
77chain 'B' and (resid 66 through 128 )BL66 - 12866 - 128
88chain 'B' and (resid 129 through 144 )BL129 - 144129 - 144
99chain 'B' and (resid 145 through 188 )BL145 - 188145 - 188

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