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- PDB-8eqo: Crystal structure of E.coli DsbA mutant K58A -

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Basic information

Entry
Database: PDB / ID: 8eqo
TitleCrystal structure of E.coli DsbA mutant 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: 1.62 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 8, 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)42,4425
Polymers42,1942
Non-polymers2483
Water8,377465
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1892
Polymers21,0971
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)21,2533
Polymers21,0971
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.635, 63.090, 74.408
Angle α, β, γ (deg.)90.000, 126.650, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-452-

HOH

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21096.922 Da / Num. of mol.: 2 / Mutation: 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.: 465 / 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: 2.63 Å3/Da / Density % sol: 53.14 %
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: 1.62→48.1 Å / Num. obs: 54574 / % possible obs: 98.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.019 / Rrim(I) all: 0.038 / Net I/σ(I): 19.7 / Num. measured all: 203208 / Scaling rejects: 11
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
1.62-1.653.70.242883523920.9280.1410.2814.188
8.89-48.13.50.0211933450.9990.0120.0234494.7

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Processing

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

1fvk


Resolution: 1.62→34.18 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1838 2738 5.02 %
Rwork0.1549 51832 -
obs0.1563 54570 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.05 Å2 / Biso mean: 27.9836 Å2 / Biso min: 12.89 Å2
Refinement stepCycle: final / Resolution: 1.62→34.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 29 465 3442
Biso mean--56.84 38.27 -
Num. residues----376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.62-1.650.22191250.18512303242888
1.65-1.680.19921440.169426082752100
1.68-1.710.21721500.185926082758100
1.71-1.750.25511620.190825652727100
1.75-1.790.21341440.17825952739100
1.79-1.830.22691150.164726322747100
1.83-1.870.20251320.164426222754100
1.87-1.920.20231410.159726282769100
1.92-1.980.20731050.161226112716100
1.98-2.050.20851220.15892602272499
2.05-2.120.21161400.16752616275699
2.12-2.20.2121260.16222582270899
2.2-2.30.19641450.15912640278599
2.3-2.420.20481470.16182557270499
2.42-2.580.19731330.15862608274199
2.58-2.780.18261430.15852600274399
2.78-3.050.18741600.162559271999
3.05-3.50.18381060.15132638274498
3.5-4.40.14371400.13052617275798
4.4-34.180.16031580.14892641279998
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)
10.1774-0.01040.37277.76032.15831.39790.04440.12460.0632-0.9645-0.21470.2459-0.29790.08970.08260.4220.0096-0.06290.2263-0.02940.23225.2862-13.2261-13.9169
22.01292.37550.49915.6129-1.48146.2761-0.26220.23560.1979-0.73320.0338-0.8379-0.52560.4670.10110.3621-0.090.0640.369-0.03050.28738.324-3.1607-9.0833
30.66770.1411-0.73611.41160.60491.6749-0.02010.1124-0.02240.01360.08020.10110.0725-0.0330.05370.2033-0.0421-0.00210.2076-0.00930.171226.8245-7.17957.7783
44.8467-1.0465-3.06342.58621.2485.0767-0.1995-0.2088-0.32190.2339-0.08950.01250.74350.46930.04750.29570.02230.00460.2596-0.01320.197829.5429-18.48584.6326
50.6190.4401-0.15223.55182.19413.044-0.04670.1007-0.2149-0.23780.1534-0.1721-0.03050.4342-0.06730.1898-0.0148-0.02410.2762-0.02660.236535.7127-7.54333.446
62.26540.39620.04721.2815-0.01091.8705-0.06090.01-0.02280.0550.073-0.00030.03980.04070.00010.1398-0.0297-0.01920.17080.00180.132332.8463-3.574718.6211
72.38561.9345-0.76493.5738-1.42052.5461-0.0593-0.2606-0.2270.1093-0.0155-0.4366-0.0250.5340.04350.1674-0.0128-0.02590.25730.00790.199944.1121-1.906522.7837
83.45050.24162.98210.84960.07034.3883-0.09540.37460.128-0.12720.0231-0.1216-0.21480.37680.02280.2206-0.10480.02070.2912-0.00580.187742.02323.06665.5417
91.59320.5858-1.24343.33451.07424.1124-0.06680.17-0.1042-0.5320.1414-0.072-0.15010.163-0.00030.2387-0.04710.00240.2354-0.0170.163231.1788-4.0523-5.2807
100.1028-0.420.40033.0236-3.36363.8414-0.25680.26110.1576-0.02250.18080.97140.2545-0.7642-0.09550.287-0.07530.00910.37-0.06990.325518.2948-14.2636-4.6809
113.6895-0.5814-1.59483.53921.3453.7667-0.4655-0.0375-0.3480.04060.08060.15960.70490.02140.21230.3008-0.01360.01850.2046-0.05240.208227.7549-18.383-4.9838
122.00040.144-0.48322.0276-1.19181.99640.020.22570.1759-0.0151-0.0638-0.0487-0.03260.0650.01990.7215-0.14070.23470.5005-0.26820.859432.1738-10.25378.6888
132.7671.81230.45272.51990.75423.09440.14270.41430.2295-0.41190.01060.5889-0.6333-0.42390.26120.32180.0877-0.05250.27880.03530.32942.05029.253920.5826
141.1238-0.08790.05992.37161.33411.9546-0.04740.0381-0.00990.0053-0.01950.25670.0115-0.18910.06830.1943-0.02250.0140.1910.01360.22646.2784-7.605221.7958
152.73221.0137-0.61582.94420.45181.6642-0.15120.0732-0.1847-0.2240.0939-0.17740.09510.01040.05270.1773-0.0342-0.00470.159-0.00860.17337.7053-20.892814.3658
163.7740.48551.49222.3390.00914.5366-0.19920.2019-0.2937-0.4110.22120.0860.2799-0.31130.11790.2065-0.09610.01540.2762-0.03390.206-2.2852-27.61911.7505
172.34471.8075-0.76216.0417-0.26522.4819-0.14510.25350.356-0.55980.14380.6452-0.274-0.44170.1870.25420.0062-0.16360.35480.05230.2565-4.6867-10.01748.5493
182.86380.3014-0.1112.92131.45763.60520.0396-0.04280.2908-0.45790.00270.0612-0.6053-0.0532-0.05240.25-0.01050.01640.17340.02680.25527.97553.469219.9785
193.14791.04520.26763.14140.42075.1897-0.0333-0.10850.32130.09320.00160.4261-0.0079-0.2555-0.00540.216-0.00020.06690.1461-0.00940.26675.5473.32330.1965
202-9.574722-6.81982-0.56072.4825-3.7407-1.50270.1575-0.59860.86661.04940.37470.42140.1911-0.13040.6138-0.06190.65945.7915-11.884221.3062
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 65 )B22 - 65
15X-RAY DIFFRACTION15chain 'B' and (resid 66 through 114 )B66 - 114
16X-RAY DIFFRACTION16chain 'B' and (resid 115 through 128 )B115 - 128
17X-RAY DIFFRACTION17chain 'B' and (resid 129 through 144 )B129 - 144
18X-RAY DIFFRACTION18chain 'B' and (resid 145 through 170 )B145 - 170
19X-RAY DIFFRACTION19chain 'B' and (resid 171 through 188 )B171 - 188
20X-RAY DIFFRACTION20chain 'B' and (resid 201 through 201 )B201

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