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- PDB-9egr: Crystal structure of oxidised E.coli DsbA in complex with allene -

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Basic information

Entry
Database: PDB / ID: 9egr
TitleCrystal structure of oxidised E.coli DsbA in complex with allene
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / Oxidoreductase inhibitor
Function / homology
Function and homology information


disulfide oxidoreductase activity / 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
: / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsBalaji, G.R. / Tasdan, Y. / Ilyichova, O.V. / Akhtar, N. / Scanlon, M.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Identification of an Allene Warhead That Selectively Targets a Histidine Residue in the Escherichia coli Oxidoreductase Enzyme DsbA.
Authors: Tasdan, Y. / Balaji, G.R. / Akhtar, N. / Ilyichova, O. / Cunliffe, T. / Heras, B. / Strat, L.L. / Murray, J. / Capuano, B. / Scanlon, M.J. / Doak, B.C.
History
DepositionNov 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)46,5613
Polymers46,2592
Non-polymers3021
Water9,710539
1
A: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)23,1291
Polymers23,1291
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)23,4322
Polymers23,1291
Non-polymers3021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.451, 65.114, 93.957
Angle α, β, γ (deg.)90.000, 93.861, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 23129.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dsbA, Z5392, ECs4783 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEG5
#2: Chemical ChemComp-A1BH7 / methyl 4-{3-[(5-methyl-1,2-oxazole-3-carbonyl)amino]phenyl}butanoate


Mass: 302.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.49 Å3/Da / Density % sol: 50.58 % / Description: Rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 24% (w/v) PEG4000, 14% (v/v) glycerol, 0.035 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 2, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.62→37.64 Å / Num. obs: 57277 / % possible obs: 99.3 % / Redundancy: 7.1 % / Biso Wilson estimate: 18.46 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.2
Reflection shellResolution: 1.62→1.65 Å / Num. unique obs: 177 / CC1/2: 0.56

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→37.64 Å / SU ML: 0.2142 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.9021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2192 2799 4.9 %
Rwork0.1898 54317 -
obs0.1913 57116 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.1 Å2
Refinement stepCycle: LAST / Resolution: 1.62→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 22 539 3487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643076
X-RAY DIFFRACTIONf_angle_d0.78194175
X-RAY DIFFRACTIONf_chiral_restr0.0468453
X-RAY DIFFRACTIONf_plane_restr0.0056549
X-RAY DIFFRACTIONf_dihedral_angle_d16.00011114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.650.32761310.29562676X-RAY DIFFRACTION98.46
1.65-1.680.2791430.26512723X-RAY DIFFRACTION98.56
1.68-1.710.32411420.24512706X-RAY DIFFRACTION98.75
1.71-1.750.26011370.24192679X-RAY DIFFRACTION98.84
1.75-1.780.26261080.22662700X-RAY DIFFRACTION98.91
1.78-1.820.24861410.21912704X-RAY DIFFRACTION98.96
1.82-1.870.25951340.21772745X-RAY DIFFRACTION99.07
1.87-1.920.35191310.28152684X-RAY DIFFRACTION98.39
1.92-1.980.2731180.24632702X-RAY DIFFRACTION97.85
1.98-2.040.23191250.20972750X-RAY DIFFRACTION99.17
2.04-2.110.22871310.20552675X-RAY DIFFRACTION98.18
2.11-2.20.22191580.19082692X-RAY DIFFRACTION98.41
2.2-2.30.25481560.23142618X-RAY DIFFRACTION96.42
2.3-2.420.21361500.18332741X-RAY DIFFRACTION99.83
2.42-2.570.22431490.18822735X-RAY DIFFRACTION99.76
2.57-2.770.22141430.18592758X-RAY DIFFRACTION99.93
2.77-3.050.20871510.18162736X-RAY DIFFRACTION99.9
3.05-3.490.21481590.17422743X-RAY DIFFRACTION99.83
3.49-4.40.17711520.14672713X-RAY DIFFRACTION98.15
4.4-37.640.16271400.15262837X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 0.495629348666 Å / Origin y: -5.67798645966 Å / Origin z: 22.3954048482 Å
111213212223313233
T0.134756902997 Å20.00161601312158 Å2-0.00603691336148 Å2-0.137227054584 Å20.00333968582798 Å2--0.126436141821 Å2
L0.43171122415 °20.078328648274 °20.0230019678538 °2-0.500873744132 °20.294646411826 °2--0.597380075035 °2
S0.0330220713824 Å °0.0252069077269 Å °0.0175379683646 Å °-0.0502452118933 Å °-0.0130133781894 Å °-0.0233117015672 Å °-0.0257066012407 Å °-0.0106304631205 Å °-0.0187627188056 Å °
Refinement TLS groupSelection details: all

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