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- PDB-8uf9: EcDsbA in complex with 2-benzyl-4-phenylthiazole-5-carboxylic acid -

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Basic information

Entry
Database: PDB / ID: 8uf9
TitleEcDsbA in complex with 2-benzyl-4-phenylthiazole-5-carboxylic acid
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / Inhibitors / Complex
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: 2.16 Å
AuthorsWang, G. / Heras, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1099151 Australia
CitationJournal: To Be Published
Title: Two-mode inhibition of DsbA: combination of two site-specific inhibitors enhances virulence inhibition in Salmonella enterica serovar Typhimurium
Authors: Wang, G. / Heras, B.
History
DepositionOct 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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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)42,6694
Polymers42,3102
Non-polymers3592
Water5,314295
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4502
Polymers21,1551
Non-polymers2951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2192
Polymers21,1551
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.630, 63.560, 96.340
Angle α, β, γ (deg.)90.00, 141.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21155.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEG4
#2: Chemical ChemComp-W9H / 2-benzyl-4-phenyl-1,3-thiazole-5-carboxylic acid


Mass: 295.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13NO2S / Feature type: SUBJECT OF INVESTIGATION
#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.: 295 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.16→34.8 Å / Num. obs: 23560 / % possible obs: 97.9 % / Redundancy: 3.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.055 / Rrim(I) all: 0.11 / Net I/σ(I): 9 / Num. measured all: 92157
Reflection shellResolution: 2.16→2.28 Å / % possible obs: 97.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.376 / Num. measured all: 13470 / Num. unique obs: 3434 / CC1/2: 0.868 / Rpim(I) all: 0.215 / Rrim(I) all: 0.435 / Net I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 2.16→33.33 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 1241 5.27 %
Rwork0.1729 --
obs0.176 23558 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→33.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 22 295 3273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083065
X-RAY DIFFRACTIONf_angle_d0.9554145
X-RAY DIFFRACTIONf_dihedral_angle_d16.5741124
X-RAY DIFFRACTIONf_chiral_restr0.037446
X-RAY DIFFRACTIONf_plane_restr0.004542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1601-2.24660.31291480.22432454X-RAY DIFFRACTION97
2.2466-2.34880.32221670.22642448X-RAY DIFFRACTION98
2.3488-2.47260.24021220.19722444X-RAY DIFFRACTION97
2.4726-2.62740.26341130.20222495X-RAY DIFFRACTION98
2.6274-2.83020.29291330.19272479X-RAY DIFFRACTION98
2.8302-3.11480.25381580.19212451X-RAY DIFFRACTION98
3.1148-3.56510.22851410.17162489X-RAY DIFFRACTION97
3.5651-4.48990.17981200.13562524X-RAY DIFFRACTION98
4.4899-33.330.18291390.14642533X-RAY DIFFRACTION97

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