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- PDB-8eqr: Crystal structure of E.coli DsbA mutant E24A -

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Basic information

Entry
Database: PDB / ID: 8eqr
TitleCrystal structure of E.coli DsbA mutant E24A
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
DI(HYDROXYETHYL)ETHER / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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 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

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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)84,6006
Polymers84,3884
Non-polymers2122
Water10,106561
1
A: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)21,0971
Polymers21,0971
Non-polymers00
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)21,2032
Polymers21,0971
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)21,0971
Polymers21,0971
Non-polymers00
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)21,2032
Polymers21,0971
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.830, 108.658, 118.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Thiol:disulfide interchange protein DsbA


Mass: 21096.988 Da / Num. of mol.: 4 / Mutation: E24A
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-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.08 Å3/Da / Density % sol: 60.09 %
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 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 46940 / % possible obs: 98.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.082 / Rrim(I) all: 0.207 / Χ2: 0.823 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.345.60.60822390.5710.270.6690.39795.7
2.34-2.385.40.54822610.8690.2490.6060.40695.8
2.38-2.435.70.53622600.7280.2380.590.39597.2
2.43-2.486.10.522860.880.2160.5470.40996.9
2.48-2.535.80.43822780.9190.1930.4810.44797.3
2.53-2.596.40.41322890.9240.1730.450.45898.5
2.59-2.666.70.3523180.9540.1450.3810.598.6
2.66-2.736.80.36523340.9420.1530.3980.50599
2.73-2.816.80.31223160.9530.1310.340.57599.3
2.81-2.96.80.30623600.9580.130.3340.60699.6
2.9-36.90.29523620.9690.1250.3210.66499.6
3-3.126.90.30423450.9620.130.3310.69899.7
3.12-3.266.70.25523570.9690.110.2790.90499.8
3.26-3.446.30.22623660.9780.1010.2481.0499.8
3.44-3.656.60.18423780.9810.0820.2021.24299.8
3.65-3.936.80.16223850.980.0720.1781.35999.4
3.93-4.337.20.13823710.9890.0580.151.45899.7
4.33-4.957.10.11824270.9910.050.1281.41499.6
4.95-6.246.80.1324500.9890.0570.1431.11599.8
6.24-506.60.07625580.9960.0330.0831.24399.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 2.29→42.14 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 2535 5.42 %
Rwork0.2167 44240 -
obs0.219 46775 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.55 Å2 / Biso mean: 36.3271 Å2 / Biso min: 15.13 Å2
Refinement stepCycle: final / Resolution: 2.29→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5860 0 34 561 6455
Biso mean--47.76 41.13 -
Num. residues----749
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.330.30561290.28422129225887
2.33-2.380.31811550.25842345250096
2.38-2.430.32291480.25322398254698
2.43-2.490.28861180.24622380249897
2.49-2.550.25171450.23122443258898
2.55-2.620.27161530.23462412256598
2.62-2.70.27071350.22712454258999
2.7-2.780.26471270.22652492261999
2.78-2.880.29441520.21962458261099
2.88-30.32531550.22662472262799
3-3.140.2781290.233124902619100
3.14-3.30.24531200.227225192639100
3.3-3.510.28681270.20962512263999
3.51-3.780.23841620.201324592621100
3.78-4.160.26971550.189525082663100
4.16-4.760.19881550.178525352690100
4.76-5.990.22551450.213825612706100
5.99-42.140.24051250.22152673279898

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