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- PDB-8eqp: Crystal structure of E.coli DsbA mutant E24A/E37A/K58A -

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Basic information

Entry
Database: PDB / ID: 8eqp
TitleCrystal structure of E.coli DsbA mutant E24A/E37A/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
CITRATE ANION / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, G. / Heras, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) 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 9, 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 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
C: Thiol:disulfide interchange protein DsbA
D: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,67010
Polymers83,9234
Non-polymers7476
Water7,422412
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2623
Polymers20,9811
Non-polymers2812
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)21,2623
Polymers20,9811
Non-polymers2812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0732
Polymers20,9811
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0732
Polymers20,9811
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.262, 80.217, 105.734
Angle α, β, γ (deg.)90.000, 93.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thiol:disulfide interchange protein DsbA


Mass: 20980.852 Da / Num. of mol.: 4 / Mutation: E24A, E37A, 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15-20% PEG8000, 0.1M phosphate-citrate, pH 3.8-4.4, 0.2M NaCl

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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: Oct 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→105.53 Å / Num. obs: 59879 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.074 / Rrim(I) all: 0.143 / Net I/σ(I): 6.3 / Num. measured all: 219355 / Scaling rejects: 51
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
2.1-2.163.50.6961591545170.750.4310.8221.797.4
9.14-105.533.70.0728477730.9590.0420.0821599.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fvk

1fvk


Resolution: 2.3→61.14 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 2346 5.15 %
Rwork0.1961 43216 -
obs0.1989 45562 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.92 Å2 / Biso mean: 33.7145 Å2 / Biso min: 15.8 Å2
Refinement stepCycle: final / Resolution: 2.3→61.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5864 0 92 412 6368
Biso mean--45.26 34.75 -
Num. residues----749
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.350.29711340.232325652699100
2.35-2.40.28911560.226424772633100
2.4-2.450.31191640.23425232687100
2.45-2.520.28761460.216325142660100
2.52-2.580.27771260.212225192645100
2.58-2.660.24711510.202125582709100
2.66-2.740.30991270.214224832610100
2.75-2.840.23181400.209725232663100
2.84-2.960.27951430.215525582701100
2.96-3.090.26461590.214325172676100
3.09-3.250.28931320.211125442676100
3.25-3.460.28851000.210825662666100
3.46-3.730.23661450.177425392684100
3.73-4.10.22531380.170125622700100
4.1-4.690.19951250.159625582683100
4.69-5.910.21831200.184925952715100
5.91-61.140.2381400.19122615275599
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)
12.4373-0.63450.68942.5209-1.10452.7670.1540.13430.0844-0.0504-0.2889-0.3510.10850.35530.07750.22910.0170.00750.2720.05330.2159-24.166422.1168-13.9319
23.86940.6766-0.46313.6846-0.93770.24220.02940.0861-0.1817-0.1317-0.0168-0.53530.08330.00390.1360.22580.0302-0.04070.23940.00110.3145-24.68813.8627-14.2281
33.8982-2.18990.37853.1970.68080.92540.20730.1236-0.3434-0.2976-0.15740.4323-0.0207-0.0841-0.01830.3053-0.0146-0.09610.21080.03670.322-38.65167.1387-11.3489
45.2627-1.56160.81810.4745-0.25080.13740.22191.1082-1.7068-0.7821-0.11591.33950.64990.0765-0.32090.5153-0.0973-0.25030.3535-0.05880.6916-36.4048-4.2809-14.7945
52.93381.97731.27824.56692.93042.64780.24280.062-0.354-0.1515-0.3047-0.45780.43880.26910.08690.34010.0762-0.06660.25910.04480.2552-21.85433.6743-7.7393
62.164-0.34370.51352.98-0.74881.291-0.06820.25630.2519-0.2448-0.2695-0.4998-0.02260.25640.28060.2178-0.00560.01380.30910.08450.2803-22.010526.2385-14.3013
73.40740.2943-0.15692.4811.50043.1159-0.1031-0.2501-0.12460.2535-0.15970.16630.1603-0.22440.20260.2778-0.0243-0.01210.2445-0.01550.2398-11.711810.577-55.4431
80.9123-0.2414-0.25592.3591.10441.61750.02580.03470.0404-0.1229-0.075-0.0029-0.1706-0.11860.05230.21550.0059-0.03930.2317-0.0170.1751-7.201918.2708-59.4651
92.27593.11721.83596.0149-0.11855.4554-0.012-0.19850.76150.1045-0.37031.1584-1.0424-1.1667-0.18460.41590.2726-0.16240.29730.27450.7652-21.77253.426-38.3236
102.67831.0414-0.4342.56561.46381.5507-0.04230.20460.3222-0.085-0.02320.27290.0046-0.05620.07780.24240.0488-0.05060.22520.03890.1933-7.327342.0314-37.354
111.9533-0.35370.93581.30060.01860.67190.0344-0.238-0.10230.1276-0.01260.1356-0.1376-0.01520.04230.27330.0031-0.00290.19590.00890.2503-9.298440.6583-30.6728
121.60550.71090.162.6428-0.54831.42480.02870.0382-0.06420.049-0.0371-0.03330.00970.0105-0.00660.2340.0207-0.0380.19630.01570.18295.678833.8219-30.9966
131.81870.62310.06774.26673.26892.58470.205-0.4649-0.19150.45550.0866-0.23511.06320.3475-0.20620.33630.0661-0.09380.24080.02270.2984.910621.5104-29.9533
142.51-2.14741.68476.1593-3.98422.79140.06510.4067-0.1530.06-0.15590.0677-0.11150.1290.17080.2235-0.0075-0.05070.2158-0.03010.1675-5.963928.0518-42.5143
153.66650.41410.82783.93920.45992.38740.06690.07510.1195-0.28440.03820.4992-0.2039-0.3869-0.13430.24760.0649-0.00680.25880.0790.2238-13.100243.3097-41.8787
162.21-0.5006-0.14934.08932.05972.0020.3188-0.36951.2246-0.4940.0307-0.6928-1.18090.7919-0.2510.5585-0.00750.11820.2861-0.10150.6192-11.462757.4845-33.7468
172.94940.7148-0.0955.99640.46233.97940.1673-0.2170.55960.46690.00420.9446-0.0984-0.2051-0.14150.29590.06560.08390.30650.01470.4346-17.342449.8176-29.696
182.36060.3168-1.05472.26320.04672.9231-0.0047-0.5007-0.33430.4641-0.12850.28890.3770.08510.06660.319-0.0569-0.00060.27280.06880.25869.463925.46313.6047
192.83121.2337-0.52082.4977-0.03142.15480.1866-0.05060.18020.1634-0.15270.394-0.093-0.2653-0.02280.2833-0.0314-0.03080.23340.01230.29955.092730.2307-2.2827
201.158-0.37650.01912.77480.74472.76720.066-0.00720.08950.06540.02020.04210.0890.0606-0.08960.1819-0.0066-0.03610.20480.01190.213314.219837.0293-14.2817
213.2892.39261.50073.80863.26643.4871-0.37880.34230.5468-0.72720.16370.3687-1.0298-0.40640.21490.4082-0.0026-0.07950.22680.03760.298912.474249.0843-14.6231
222.6489-1.52461.0195.102-2.30543.81060.1276-0.28570.1640.6199-0.0598-0.2067-0.2491-0.2425-0.03690.2118-0.0439-0.03080.2271-0.03690.197516.75142.91461.6992
234.01270.4342-0.91993.96830.48844.8226-0.0714-0.52910.02730.7175-0.2985-0.1068-0.0467-0.12690.40150.2985-0.0663-0.00060.32430.06130.235912.057527.57157.3106
245.01110.98961.72093.4807-1.40753.1552-0.0808-0.2399-0.59580.55620.11330.18730.5819-0.3075-0.07880.373-0.15560.12570.3940.06220.47521.991618.64592.9203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 49 )A1 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 65 )A50 - 65
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 114 )A66 - 114
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 128 )A115 - 128
5X-RAY DIFFRACTION5chain 'A' and (resid 129 through 144 )A129 - 144
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 188 )A145 - 188
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 65 )B1 - 65
8X-RAY DIFFRACTION8chain 'B' and (resid 66 through 188 )B66 - 188
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 11 )C1 - 11
10X-RAY DIFFRACTION10chain 'C' and (resid 12 through 38 )C12 - 38
11X-RAY DIFFRACTION11chain 'C' and (resid 39 through 65 )C39 - 65
12X-RAY DIFFRACTION12chain 'C' and (resid 66 through 115 )C66 - 115
13X-RAY DIFFRACTION13chain 'C' and (resid 116 through 128 )C116 - 128
14X-RAY DIFFRACTION14chain 'C' and (resid 129 through 144 )C129 - 144
15X-RAY DIFFRACTION15chain 'C' and (resid 145 through 161 )C145 - 161
16X-RAY DIFFRACTION16chain 'C' and (resid 162 through 170 )C162 - 170
17X-RAY DIFFRACTION17chain 'C' and (resid 171 through 188 )C171 - 188
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 38 )D1 - 38
19X-RAY DIFFRACTION19chain 'D' and (resid 39 through 65 )D39 - 65
20X-RAY DIFFRACTION20chain 'D' and (resid 66 through 114 )D66 - 114
21X-RAY DIFFRACTION21chain 'D' and (resid 115 through 128 )D115 - 128
22X-RAY DIFFRACTION22chain 'D' and (resid 129 through 144 )D129 - 144
23X-RAY DIFFRACTION23chain 'D' and (resid 145 through 161 )D145 - 161
24X-RAY DIFFRACTION24chain 'D' and (resid 162 through 188 )D162 - 188

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