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- PDB-8u59: EcDsbA soaked with N-(2-fluorophenyl)-5-methylisoxazole-3-carboxa... -

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Basic information

Entry
Database: PDB / ID: 8u59
TitleEcDsbA soaked with N-(2-fluorophenyl)-5-methylisoxazole-3-carboxamide and N-(4-(thiophen-3-yl)benzyl)cyclohexanamine
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: 1.77 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 12, 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

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)42,8655
Polymers42,3102
Non-polymers5553
Water5,188288
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4262
Polymers21,1551
Non-polymers2711
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)21,4393
Polymers21,1551
Non-polymers2842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.518, 64.655, 74.441
Angle α, β, γ (deg.)90.00, 125.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-419-

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-5V9 / ~{N}-[(4-thiophen-3-ylphenyl)methyl]cyclohexanamine


Mass: 271.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21NS / Feature type: SUBJECT OF INVESTIGATION
#3: 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
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: Nov 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.77→48.76 Å / Num. obs: 43287 / % possible obs: 99.4 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.024 / Rrim(I) all: 0.048 / Χ2: 1.07 / Net I/σ(I): 16.4 / Num. measured all: 165799
Reflection shellResolution: 1.77→1.8 Å / % possible obs: 92.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.865 / Num. measured all: 8707 / Num. unique obs: 2289 / CC1/2: 0.64 / Rpim(I) all: 0.5 / Rrim(I) all: 1.002 / Χ2: 1.12 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→48.76 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 2134 4.93 %
Rwork0.1849 --
obs0.1867 43264 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 36 288 3198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082985
X-RAY DIFFRACTIONf_angle_d1.0654054
X-RAY DIFFRACTIONf_dihedral_angle_d13.628412
X-RAY DIFFRACTIONf_chiral_restr0.048446
X-RAY DIFFRACTIONf_plane_restr0.006528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.32821280.30582586X-RAY DIFFRACTION95
1.81-1.860.32461430.28412772X-RAY DIFFRACTION100
1.86-1.910.27361320.25332754X-RAY DIFFRACTION100
1.91-1.960.2791310.24612733X-RAY DIFFRACTION100
1.96-2.020.26851500.23252717X-RAY DIFFRACTION100
2.02-2.10.32061400.23472761X-RAY DIFFRACTION100
2.1-2.180.26041340.21732763X-RAY DIFFRACTION100
2.18-2.280.27071450.20662739X-RAY DIFFRACTION100
2.28-2.40.25091250.20032775X-RAY DIFFRACTION100
2.4-2.550.21931760.20192705X-RAY DIFFRACTION100
2.55-2.750.22481650.19482740X-RAY DIFFRACTION100
2.75-3.020.25921610.19032732X-RAY DIFFRACTION100
3.02-3.460.21631340.17732786X-RAY DIFFRACTION100
3.46-4.360.18471300.15072756X-RAY DIFFRACTION99
4.36-48.760.16891400.15422811X-RAY DIFFRACTION99
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)
11.01310.56981.29275.25743.81293.50950.03390.2755-0.1838-0.27840.0391-0.0780.08250.0189-0.0320.2913-0.05110.00690.2585-0.03540.235630.5275-10.19681.218
21.99671.22631.34772.61451.86612.5147-0.06950.1295-0.0843-0.12810.0697-0.0323-0.00370.0912-0.01440.2081-0.0333-0.00370.18460.01550.187732.8564-5.65239.3841
32.3601-0.1257-0.29472.88211.54595.02230.35860.05580.4097-0.2374-0.13720.1545-0.6617-0.5741-0.18150.28890.02390.0490.3083-0.00830.32644.4659-2.837621.0304
42.19960.5513-1.14174.00310.60772.6255-0.02760.1070.0592-0.3112-0.00090.2417-0.1793-0.3340.02540.20280.0189-0.04280.27470.01450.18133.8653-16.021813.5597
53.6945-0.1964-0.05996.5135-1.98538.69370.3941-0.45060.756-0.37590.0477-0.2599-1.52220.017-0.29840.5660.01670.21010.278-0.08560.4257.67454.669628.8329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 188 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 65 )
4X-RAY DIFFRACTION4chain 'B' and (resid 66 through 161 )
5X-RAY DIFFRACTION5chain 'B' and (resid 162 through 188 )

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