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- PDB-8ubq: EcDsbA soaked with N-(2-fluorophenyl)-5-methylisoxazole-3-carboxa... -

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Basic information

Entry
Database: PDB / ID: 8ubq
TitleEcDsbA soaked with N-(2-fluorophenyl)-5-methylisoxazole-3-carboxamide and 2-benzyl-4-phenylthiazole-5-carboxylic acid
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / Inhibitor
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 / Chem-SW0 / : / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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
DepositionSep 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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

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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)42,8895
Polymers42,3102
Non-polymers5793
Water5,801322
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)21,4393
Polymers21,1551
Non-polymers2842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.971, 64.760, 74.842
Angle α, β, γ (deg.)90.00, 125.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-441-

HOH

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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: Chemical ChemComp-SW0 / N-(2-fluorophenyl)-5-methyl-1,2-oxazole-3-carboxamide


Mass: 220.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9FN2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion
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: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→48.92 Å / Num. obs: 30063 / % possible obs: 98.9 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.018 / Rrim(I) all: 0.04 / Χ2: 1.04 / Net I/σ(I): 24.7 / Num. measured all: 129569
Reflection shellResolution: 2→2.05 Å / % possible obs: 91 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.079 / Num. measured all: 7966 / Num. unique obs: 2030 / CC1/2: 0.991 / Rpim(I) all: 0.045 / Rrim(I) all: 0.091 / Χ2: 0.95 / Net I/σ(I) obs: 12.1

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→33.101 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 1572 5.23 %
Rwork0.1793 --
obs0.1816 30057 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→33.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 38 322 3310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083069
X-RAY DIFFRACTIONf_angle_d0.8344152
X-RAY DIFFRACTIONf_dihedral_angle_d5.9842175
X-RAY DIFFRACTIONf_chiral_restr0.05445
X-RAY DIFFRACTIONf_plane_restr0.005542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.06550.27051010.20382442X-RAY DIFFRACTION93
2.0655-2.13930.22741270.20232627X-RAY DIFFRACTION100
2.1393-2.2250.31111440.20182588X-RAY DIFFRACTION100
2.225-2.32620.25781580.20082553X-RAY DIFFRACTION99
2.3262-2.44880.26961520.20742611X-RAY DIFFRACTION100
2.4488-2.60220.29141660.20462600X-RAY DIFFRACTION100
2.6022-2.8030.25671150.19712628X-RAY DIFFRACTION100
2.803-3.08490.19221270.20042617X-RAY DIFFRACTION99
3.0849-3.53090.23781680.18352587X-RAY DIFFRACTION99
3.5309-4.44680.20061700.14892585X-RAY DIFFRACTION99
4.4468-33.1010.17131440.1552647X-RAY DIFFRACTION98

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