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- PDB-8eoc: Crystal structure of E.coli DsbA mutant E24A/K58A -

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Basic information

Entry
Database: PDB / ID: 8eoc
TitleCrystal structure of E.coli DsbA mutant E24A/K58A
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / DsbA mutant / thioredoxin-family 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: 1.47 Å
AuthorsWang, G. / Heras, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1144046 Australia
CitationJournal: Antioxidants / Year: 2023
Title: A Buried Water Network Modulates the Activity of the Escherichia coli Disulphide Catalyst DsbA.
Authors: Wang, G. / Qin, J. / Verderosa, A.D. / Hor, L. / Santos-Martin, C. / Paxman, J.J. / Martin, J.L. / Totsika, M. / Heras, B.
History
DepositionOct 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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)42,3265
Polymers42,0782
Non-polymers2483
Water6,359353
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1312
Polymers21,0391
Non-polymers921
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)21,1953
Polymers21,0391
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.013, 63.590, 74.716
Angle α, β, γ (deg.)90.000, 126.770, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21038.887 Da / Num. of mol.: 2 / Mutation: E24A, K58A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEG4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 353 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.67 Å3/Da / Density % sol: 53.91 %
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: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.47→48.41 Å / Num. obs: 74603 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.028 / Rrim(I) all: 0.056 / Net I/σ(I): 11.2 / Num. measured all: 279376 / Scaling rejects: 17
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
1.47-1.493.60.7671175932630.6610.4540.8941.487.6
8.04-48.413.50.03216534700.9970.0190.03828.794.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.47→37.32 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1967 3784 5.07 %
Rwork0.1762 70800 -
obs0.1773 74584 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.77 Å2 / Biso mean: 33.1846 Å2 / Biso min: 15.41 Å2
Refinement stepCycle: final / Resolution: 1.47→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 29 353 3322
Biso mean--65.05 39.24 -
Num. residues----376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.490.34181210.30242234235584
1.49-1.510.31651510.263626312782100
1.51-1.530.26221530.257826302783100
1.53-1.550.26361670.243926072774100
1.55-1.570.29091520.223826382790100
1.57-1.60.21411560.213526422798100
1.6-1.620.25441440.221326512795100
1.62-1.650.24881460.216226432789100
1.65-1.680.25721230.220926462769100
1.68-1.710.23871350.216126442779100
1.71-1.750.25661360.209526572793100
1.75-1.790.22241210.196826612782100
1.79-1.830.22061130.185426972810100
1.83-1.870.2111320.191426732805100
1.87-1.920.24571330.184326572790100
1.92-1.980.18351240.19442618274299
1.98-2.040.21091400.19352643278399
2.04-2.120.1951570.18632599275699
2.12-2.20.19921590.17842616277599
2.2-2.30.20581140.1792632274698
2.3-2.420.20791310.1822610274198
2.42-2.580.23781340.18812636277098
2.58-2.770.20161340.17272602273697
2.77-3.050.21331620.17632584274698
3.05-3.490.15221220.16262624274698
3.49-4.40.15541730.14252627280098
4.4-37.320.18971510.16372698284998
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)
10.6710.19110.5542.292.1842.28080.16450.1360.0378-0.9024-0.26820.6792-0.4329-0.03890.06640.49770.053-0.10120.2783-0.07990.35925.3379-13.3418-13.7878
23.19513.23940.24479.6377-2.59682.4522-0.32770.45260.3306-0.7224-0.2791-0.9202-0.58430.73620.36040.443-0.05230.0990.5327-0.04670.29838.3433-3.1063-9.2371
32.59540.1225-0.60362.34361.10383.6603-0.03740.1438-0.1713-0.08280.01510.14670.0428-0.09540.06030.2023-0.0366-0.00320.1618-0.01330.16726.8432-7.13257.9032
44.8437-0.3138-2.33152.80971.51396.1122-0.3334-0.1166-0.54560.1304-0.0509-0.06770.89620.50910.04190.34830.02910.01340.2521-0.01580.306730.1209-18.64385.1481
52.2699-0.0261-0.56554.85472.46764.7296-0.1440.2028-0.3353-0.18720.3032-0.20360.11080.6018-0.10950.2094-0.0278-0.00960.3082-0.04310.272135.8583-7.52683.4787
64.10520.3780.37991.76570.18482.7022-0.058-0.0355-0.04850.06080.0718-0.01120.04520.1383-0.02050.1826-0.0321-0.01580.17210.00020.150432.9268-3.412418.6798
74.81383.6617-1.65579.5477-3.14095.3072-0.1688-0.2784-0.28930.3248-0.0258-0.56830.01050.68350.1750.19260.0051-0.03820.299-0.00060.213544.1895-1.724622.8958
82.2016-0.62832.59790.96-0.28564.223-0.13850.51420.2372-0.25480.1636-0.1956-0.27410.49890.02370.2826-0.17020.03750.4255-0.01690.206842.23093.11885.5672
93.60581.3412-2.20414.71690.89068.0657-0.07050.4147-0.0011-0.72970.0524-0.0243-0.33950.14690.0320.2782-0.0582-0.00120.2962-0.01560.170231.2679-4.5895-5.2392
103.17671.4630.31687.3942-3.55846.7891-0.47280.3959-0.0488-0.36580.2551.70320.5006-1.430.02990.3917-0.0755-0.00470.5187-0.13120.521818.4188-14.5283-4.4374
118.0343-0.8413-4.63794.08871.29526.862-0.50750.0831-0.4910.0055-0.07830.52770.7459-0.21050.62350.34280.01530.01750.2366-0.11440.270528.038-18.448-4.8091
1222-1.19772-2.71982-0.3216-1.28453.70491.49470.1082-2.8588-0.56731.17760.21490.6996-0.01080.11780.2797-0.04940.689532.3413-10.34488.8219
134.74951.92221.79593.89810.67716.13220.22810.39560.3599-0.54510.00030.6908-1.0167-0.6987-0.11840.5030.19750.02160.39320.03780.44061.84449.251120.3534
141.55460.3084-0.15382.67191.35373.7008-0.0073-0.0092-0.0040.00170.0810.0256-0.0891-0.1688-0.07630.1873-0.02570.00220.18190.01640.210410.5339-9.03819.0882
155.8002-1.4295-2.51353.70082.19364.6234-0.116-0.1923-0.24510.4807-0.0430.5640.3797-0.13310.04610.3132-0.02360.09530.20720.0070.33726.6532-6.529330.507
161.6067-0.4564-0.5463.70891.82974.65240.1649-0.03540.4463-0.1448-0.170.5723-0.2245-0.62810.0850.1912-0.0310.00860.38290.01740.38610.8171-6.648318.7552
176.27581.6386-0.98574.81910.46071.2434-0.19220.6690.169-0.65310.16450.3604-0.0517-0.28370.06770.2624-0.0726-0.07320.28160.0070.21432.9884-17.350410.8006
184.72851.809-1.85134.2055-0.0482.0292-0.1312-0.0372-0.5027-0.0714-0.056-0.40.14850.00220.16450.2171-0.04440.00210.21460.01140.253810.2142-22.804216.3845
196.10410.16673.15852.5954-0.39217.4054-0.36380.3753-0.4305-0.41060.31560.23580.5118-0.74360.0480.2484-0.15430.01590.3876-0.02620.2374-2.1907-27.803511.9908
201.80471.8148-0.01174.89740.48442.5081-0.08980.18610.5555-0.8010.03751.03-0.0198-0.76340.06390.3847-0.0032-0.18070.51370.11870.4274-4.5729-10.08628.3953
213.5542-0.40051.26545.83060.70692.9326-0.00270.01810.401-0.46450.0630.7325-0.9445-0.7636-0.03540.31910.1168-0.01860.27990.07250.34583.48892.477715.7773
222.2425-0.82090.45666.6182-5.04276.46250.03450.09330.2139-0.3979-0.1586-0.8301-0.63921.04010.01990.4022-0.05930.22940.3275-0.04250.50515.47554.887126.4799
234.58350.77721.77954.4608-0.40346.80540.1522-0.19790.650.0956-0.10310.2337-0.2081-0.3409-0.11420.30720.02230.1280.1801-0.01340.35325.72443.351730.1018
247.86064.22811.77272.32580.95350.3998-1.99211.91382.3901-9.77161.87425.982-1.4378-1.28850.2170.8349-0.0109-0.1560.97920.14780.75336.1506-11.667621.3234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )A1 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 21 )A12 - 21
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 38 )A22 - 38
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 49 )A39 - 49
5X-RAY DIFFRACTION5chain 'A' and (resid 50 through 65 )A50 - 65
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 114 )A66 - 114
7X-RAY DIFFRACTION7chain 'A' and (resid 115 through 128 )A115 - 128
8X-RAY DIFFRACTION8chain 'A' and (resid 129 through 144 )A129 - 144
9X-RAY DIFFRACTION9chain 'A' and (resid 145 through 161 )A145 - 161
10X-RAY DIFFRACTION10chain 'A' and (resid 162 through 170 )A162 - 170
11X-RAY DIFFRACTION11chain 'A' and (resid 171 through 188 )A171 - 188
12X-RAY DIFFRACTION12chain 'A' and (resid 201 through 201 )A201
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 21 )B1 - 21
14X-RAY DIFFRACTION14chain 'B' and (resid 22 through 38 )B22 - 38
15X-RAY DIFFRACTION15chain 'B' and (resid 39 through 49 )B39 - 49
16X-RAY DIFFRACTION16chain 'B' and (resid 50 through 65 )B50 - 65
17X-RAY DIFFRACTION17chain 'B' and (resid 66 through 82 )B66 - 82
18X-RAY DIFFRACTION18chain 'B' and (resid 83 through 114 )B83 - 114
19X-RAY DIFFRACTION19chain 'B' and (resid 115 through 128 )B115 - 128
20X-RAY DIFFRACTION20chain 'B' and (resid 129 through 144 )B129 - 144
21X-RAY DIFFRACTION21chain 'B' and (resid 145 through 161 )B145 - 161
22X-RAY DIFFRACTION22chain 'B' and (resid 162 through 170 )B162 - 170
23X-RAY DIFFRACTION23chain 'B' and (resid 171 through 188 )B171 - 188
24X-RAY DIFFRACTION24chain 'B' and (resid 201 through 201 )B201

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