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- PDB-6pvz: E.coli DsbA in complex with benzofuran compound 28 ((6-benzyl-1-b... -

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Basic information

Entry
Database: PDB / ID: 6pvz
TitleE.coli DsbA in complex with benzofuran compound 28 ((6-benzyl-1-benzofuran-3-yl)acetic acid)
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibitor / complex / disulfide oxidoreductase / fragments / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...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-benzyl-1-benzofuran-3-yl)acetic acid / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWang, G. / Heras, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1099151 Australia
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 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / Item: _citation.title

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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)42,6404
Polymers42,3102
Non-polymers3302
Water6,323351
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4212
Polymers21,1551
Non-polymers2661
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)117.590, 63.430, 74.231
Angle α, β, γ (deg.)90.000, 125.020, 90.000
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 (strain K12) (bacteria)
Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEG4
#2: Chemical ChemComp-OZM / (6-benzyl-1-benzofuran-3-yl)acetic acid


Mass: 266.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O3 / 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.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 54.09 %
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
PH range: 6.0-6.3

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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 4, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.99→28.73 Å / Num. obs: 30860 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 20.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.032 / Rrim(I) all: 0.065 / Net I/σ(I): 15.9 / Num. measured all: 122486 / Scaling rejects: 10
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
1.99-2.043.70.297808121880.9150.1770.3474.298.8
9.1-28.733.50.02211433250.9990.0130.02636.595.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→28.728 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.13
RfactorNum. reflection% reflection
Rfree0.2004 1570 5.09 %
Rwork0.1663 --
obs0.1681 30859 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.95 Å2 / Biso mean: 26.7622 Å2 / Biso min: 8.93 Å2
Refinement stepCycle: final / Resolution: 1.99→28.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 34 351 3273
Biso mean--32.78 33.92 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042985
X-RAY DIFFRACTIONf_angle_d0.5694055
X-RAY DIFFRACTIONf_chiral_restr0.04445
X-RAY DIFFRACTIONf_plane_restr0.004529
X-RAY DIFFRACTIONf_dihedral_angle_d10.3861759
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9861-2.05020.27491780.19792583276199
2.0502-2.12340.23111060.18322696280299
2.1234-2.20840.2081170.17522666278399
2.2084-2.30890.2291260.172126722798100
2.3089-2.43050.22811500.174526422792100
2.4305-2.58270.21141300.174826582788100
2.5827-2.7820.20551420.170726702812100
2.782-3.06170.23451480.176426642812100
3.0617-3.5040.20021660.169226662832100
3.504-4.41210.16571350.137626742809100
4.4121-28.73120.16571720.16372698287099
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)
11.39850.38421.13763.72182.47122.8230.0030.2135-0.1261-0.40510.04330.0053-0.16960.0886-0.01850.1501-0.0296-0.01250.17210.00060.106431.566-10.41321.4064
22.07840.498-0.04062.83970.18722.5676-0.0032-0.09820.06270.1176-0.059-0.1768-0.04720.1310.06850.1129-0.0395-0.04710.14420.00620.086137.5569-1.249216.8686
32.58230.9426-0.32994.34871.69544.38-0.15780.26390.0325-0.51570.12920.111-0.26610.17610.01270.1755-0.0421-0.06350.208-0.01670.116727.5145-13.7141-3.6363
41.0841-0.25980.50124.34852.15322.31320.03450.01950.0341-0.1748-0.02710.3878-0.2018-0.2698-0.00060.164-0.01620.05350.14970.03230.23236.4462-1.952521.8844
52.5520.6405-0.39023.8170.01232.0964-0.10380.2537-0.1443-0.22620.08690.27270.0639-0.19370.01130.1237-0.0456-0.01090.1458-0.010.14054.6481-19.1713.2108
61.68240.26261.01113.81791.2427.7199-0.0928-0.01880.1197-0.22530.11610.2199-0.3663-0.11430.02880.2114-0.00870.07180.08310.01010.2828.01913.878225.7449
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 145 )A66 - 145
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 188 )A146 - 188
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 65 )B1 - 65
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 145 )B66 - 145
6X-RAY DIFFRACTION6chain 'B' and (resid 146 through 188 )B146 - 188

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