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- PDB-8dn0: E.coli DsbA in complex with N-(2-fluorophenyl)-5-methylisoxazole-... -

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Basic information

Entry
Database: PDB / ID: 8dn0
TitleE.coli DsbA in complex with N-(2-fluorophenyl)-5-methylisoxazole-3-carboxamide
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/INHIBITOR / Inhibitor / complex / disulfide oxidoreductase / fragments / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR 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 / Chem-SW0 / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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: E.coli DsbA in complex with N-(2-fluorophenyl)-5-methylisoxazole-3-carboxamide
Authors: Wang, G. / Heras, B.
History
DepositionJul 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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)42,8997
Polymers42,3102
Non-polymers5895
Water8,881493
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4604
Polymers21,1551
Non-polymers3053
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)114.840, 65.500, 74.890
Angle α, β, γ (deg.)90.000, 125.980, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-482-

HOH

21B-500-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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) / Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEG4

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Non-polymers , 5 types, 498 molecules

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


Mass: 220.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H9FN2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 54.34 %
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: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.26→53.54 Å / Num. obs: 119812 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.95 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.068 / Rrim(I) all: 0.133 / Net I/σ(I): 4.9 / Num. measured all: 442863 / Scaling rejects: 184
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.26-1.293.71.0252178258930.1220.6261.2071.499.9
6.92-53.543.60.04828107780.9940.0290.05619.999.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.57→37.326 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 3313 5.28 %
Rwork0.1713 59443 -
obs0.1725 62756 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.02 Å2 / Biso mean: 23.1402 Å2 / Biso min: 7.57 Å2
Refinement stepCycle: final / Resolution: 1.57→37.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 62 493 3511
Biso mean--24.36 34.12 -
Num. residues----376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.57-1.59250.28411410.25362480100
1.5925-1.61620.2561410.23132431100
1.6162-1.64150.24211330.23332489100
1.6415-1.66840.2651290.2235245899
1.6684-1.69720.27391210.22662471100
1.6972-1.7280.22871450.22212453100
1.728-1.76130.23151100.21632494100
1.7613-1.79720.23461190.2042495100
1.7972-1.83630.21911390.1952478100
1.8363-1.8790.22851320.19372458100
1.879-1.9260.20021510.18892453100
1.926-1.97810.23471360.1882465100
1.9781-2.03630.19811620.18592458100
2.0363-2.1020.22251610.18182424100
2.102-2.17710.22621390.17112476100
2.1771-2.26430.21141650.16862477100
2.2643-2.36730.19671330.16492485100
2.3673-2.49210.18421300.17162457100
2.4921-2.64820.21631190.16842519100
2.6482-2.85260.17321260.16212491100
2.8526-3.13950.18081060.16112527100
3.1395-3.59350.17861370.15112483100
3.5935-4.52620.14641540.13852496100
4.5262-37.3260.16881840.14932525100
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)
10.80580.2680.74423.42012.44852.16550.02180.1093-0.1081-0.08930.1028-0.18120.1220.0778-0.05110.1665-0.01430.01590.1231-0.00480.131830.5182-10.2651.1089
21.30140.93330.70891.66480.95880.90910.0197-0.0062-0.0733-0.0360.0065-0.09820.01230.0261-0.02760.0923-0.00760.00470.07630.02050.081532.4559-5.58429.3467
32.2253-1.2405-2.59122.95591.6023.0282-0.2082-0.46810.6458-0.05140.1408-0.0059-1.2017-0.09680.0690.44850.0781-0.11690.2305-0.0940.33263.502412.673124.131
42.7109-0.60830.34162.44580.85112.5056-0.0438-0.11620.0692-0.0237-0.07380.2211-0.1171-0.30490.08850.1031-0.0154-0.00610.12-0.02910.13463.2755-5.440520.6161
54.68630.9186-0.23482.86680.10412.1516-0.0255-0.031-0.13840.0293-0.0154-0.11810.07510.03850.03540.0920.003-0.01550.062-0.00710.07176.2623-22.384514.3523
60.61270.36251.20323.44281.6152.6258-0.148-0.05120.2447-0.3917-0.08870.4403-0.3307-0.20370.21090.13920.0237-0.04790.15570.00320.16-1.3987-4.156611.7334
72.0888-2.31142.00145.649-3.74492.8847-0.26440.15350.2848-0.1339-0.1347-0.5185-0.52080.98720.38910.1995-0.0510.00220.2511-0.01680.235113.51966.475725.9803
86.372-0.25461.62475.5608-1.40656.6575-0.0893-0.11330.1677-0.10470.02370.4162-0.2815-0.37220.04440.15720.0388-0.00920.1555-0.07210.13653.49444.034229.4043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 65 )A1 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 188 )A66 - 188
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 11 )B1 - 11
4X-RAY DIFFRACTION4chain 'B' and (resid 12 through 65 )B12 - 65
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 128 )B66 - 128
6X-RAY DIFFRACTION6chain 'B' and (resid 129 through 161 )B129 - 161
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 170 )B162 - 170
8X-RAY DIFFRACTION8chain 'B' and (resid 171 through 188 )B171 - 188

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