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- PDB-6pml: Crystal Structure of EcDsbA in complex benzyl ether 23 -

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Basic information

Entry
Database: PDB / ID: 6pml
TitleCrystal Structure of EcDsbA in complex benzyl ether 23
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / OXIDOREDUCTASE-INHIBITOR COMPLEX / OXIDOREDUCTASE
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 / Glutaredoxin / Glutaredoxin ...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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / [6-(benzyloxy)-1-benzofuran-3-yl]acetic acid / DI(HYDROXYETHYL)ETHER / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIlyichova, O.V. / Scanlon, M.J.
CitationJournal: Molecules / Year: 2019
Title: The Fragment-Based Development of a Benzofuran Hit as a New Class of Escherichia coli DsbA Inhibitors.
Authors: Duncan, L.F. / Wang, G. / Ilyichova, O.V. / Scanlon, M.J. / Heras, B. / Abbott, B.M.
History
DepositionJul 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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)42,7625
Polymers42,3102
Non-polymers4523
Water6,305350
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5433
Polymers21,1551
Non-polymers3882
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)21,2192
Polymers21,1551
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.540, 63.740, 96.190
Angle α, β, γ (deg.)90.000, 140.850, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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 (strain K12) (bacteria)
Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Plasmid: B0013 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEG4
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-OR4 / [6-(benzyloxy)-1-benzofuran-3-yl]acetic acid


Mass: 282.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O4 / 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.: 350 / 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: 2.7 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 11-13 % PEG 8000, 5-7.5% glycerol, 100mM Na Cacodylate pH6.1, 1mM CuCl2

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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: Oct 1, 2014
RadiationMonochromator: DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→53.1 Å / Num. obs: 29762 / % possible obs: 97.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.68 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.056 / Rrim(I) all: 0.108 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4161 / CC1/2: 0.675 / Rpim(I) all: 0.394 / Rrim(I) all: 0.736 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 2→34.84 Å / SU ML: 0.252 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.6782
RfactorNum. reflection% reflection
Rfree0.2207 1618 5.44 %
Rwork0.1823 --
obs0.1846 29756 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.29 Å2
Refinement stepCycle: LAST / Resolution: 2→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 29 350 3260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293021
X-RAY DIFFRACTIONf_angle_d0.53164108
X-RAY DIFFRACTIONf_chiral_restr0.0376451
X-RAY DIFFRACTIONf_plane_restr0.0034538
X-RAY DIFFRACTIONf_dihedral_angle_d7.10682414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.30451130.2642251X-RAY DIFFRACTION93.59
2.06-2.130.28841070.24462304X-RAY DIFFRACTION95.22
2.13-2.20.23551100.22982308X-RAY DIFFRACTION96.1
2.2-2.290.25711350.21962295X-RAY DIFFRACTION97.01
2.29-2.390.24181410.21012349X-RAY DIFFRACTION98.03
2.39-2.520.23381410.1942340X-RAY DIFFRACTION98.65
2.52-2.680.23121360.19792374X-RAY DIFFRACTION98.35
2.68-2.880.23381440.19782350X-RAY DIFFRACTION98.85
2.88-3.170.22481280.1872390X-RAY DIFFRACTION99.09
3.17-3.630.20931460.17162355X-RAY DIFFRACTION98.93
3.63-4.580.19011820.13812377X-RAY DIFFRACTION99.19
4.58-34.840.21251350.15922445X-RAY DIFFRACTION98.7
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)
10.8354165367270.0115323266884-0.6221064384391.931099042-1.395618906771.574445674940.0277022717860.1763234975280.100358879545-0.350103259871-0.00588541040978-0.05876132207150.196366586388-0.0022171012857-0.004561698318270.267598429305-0.01762863732460.02340828499090.2475920378960.007798990559340.17514020247927.49056421559.213946056411.28309333744
20.8312221133440.469660251764-0.2669708381911.856484824-0.8557302784730.873725713432-0.07770245691420.01367751507070.0151167920109-0.08002290715650.03966444097240.02643652629170.0639209780512-0.121116138220.04199006794730.182648975558-0.02937545103620.03013380527480.224728059473-0.01673520538520.13210426290924.82003816264.778338779589.68283986639
30.9726291751810.7534446993630.09098230794832.11722372294-0.7686931551041.563763814340.0391872539120.0878489281591-0.171823638624-0.0705076770562-0.0340840826004-0.3717766778220.1894546362180.266090849649-0.01253978228820.1868992064670.019319471081-0.03193055455720.245870289232-0.02941620324420.27855221465553.41931211398.9088924020217.0675016342
42.776507301011.59870150281-0.6435394733385.136966572550.575169692616.310371906380.04515352107550.0173738936281-0.205808321357-0.0958927487355-0.043311936845-0.05370847053650.346933423253-0.1325194606490.009962189048910.374584439421-0.00480898220044-0.2045074728590.1882536341990.02208350153160.41676626317348.8571942172-5.3982507029429.7073557263
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 2 through 161 )
4X-RAY DIFFRACTION4chain 'B' and (resid 162 through 188 )

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