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- PDB-6bqx: Crystal structure of Escherichia coli DsbA in complex with N-meth... -

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Basic information

Entry
Database: PDB / ID: 6bqx
TitleCrystal structure of Escherichia coli DsbA in complex with N-methyl-1-(4-phenoxyphenyl)methanamine
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / disulphide catalysts / thiol oxidase / virulence factor foldase
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
N-methyl-1-(4-phenoxyphenyl)methanamine / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.992 Å
AuthorsHeras, B. / Totsika, M. / Paxman, J.J. / Wang, G. / Scanlon, M.J.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP150102287 Australia
Australian Research Council (ARC)FT130100580 Australia
Australian Synchrotron Research Program Fellowship Australia
Citation
Journal: Antioxid. Redox Signal. / Year: 2018
Title: Inhibition of Diverse DsbA Enzymes in Multi-DsbA Encoding Pathogens.
Authors: Totsika, M. / Vagenas, D. / Paxman, J.J. / Wang, G. / Dhouib, R. / Sharma, P. / Martin, J.L. / Scanlon, M.J. / Heras, B.
#1: Journal: Angew. Chem. Int. Ed. Engl. / Year: 2015
Title: Application of fragment-based screening to the design of inhibitors of Escherichia coli DsbA.
Authors: Adams, L.A. / Sharma, P. / Mohanty, B. / Ilyichova, O.V. / Mulcair, M.D. / Williams, M.L. / Gleeson, E.C. / Totsika, M. / Doak, B.C. / Caria, S. / Rimmer, K. / Horne, J. / Shouldice, S.R. / ...Authors: Adams, L.A. / Sharma, P. / Mohanty, B. / Ilyichova, O.V. / Mulcair, M.D. / Williams, M.L. / Gleeson, E.C. / Totsika, M. / Doak, B.C. / Caria, S. / Rimmer, K. / Horne, J. / Shouldice, S.R. / Vazirani, M. / Headey, S.J. / Plumb, B.R. / Martin, J.L. / Heras, B. / Simpson, J.S. / Scanlon, M.J.
History
DepositionNov 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / Item: _citation.title / _citation.year
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Remark 0;THIS ENTRY 1ZET REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 4wf5 , DETERMINED BY ...;THIS ENTRY 1ZET REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 4wf5 , DETERMINED BY Adams, L.A., SHARMA, P., MOHANTY, B., ILYICHOVA, O.V., MULCAIR, M.D., WILLIAMS, M.L., GLEESON, E.C., TOTSIKA, M., DOAK, B.C., CARIA, S., RIMMER, K., SHOULDICE, S.R., VAZIRANI, M., HEADEY, S.J., PLUMB, B.R., MARTIN, J.L., HERAS, B., SIMPSON, J.S., SCANLON, M.J.

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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)42,5233
Polymers42,3102
Non-polymers2131
Water4,143230
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3682
Polymers21,1551
Non-polymers2131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)21,1551
Polymers21,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.150, 64.901, 75.416
Angle α, β, γ (deg.)90.000, 126.530, 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 (E. coli) / Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P0AEG4
#2: Chemical ChemComp-9AG / N-methyl-1-(4-phenoxyphenyl)methanamine


Mass: 213.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.1 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 4WF5
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.2
Details: 11-13% PEG 8000, 5-7.5% glycerol, 1 mM CuCl2, 100 mM sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953732 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 30896 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.052 / Χ2: 1.077 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.99-2.023.30.48615481.126199
2.02-2.063.30.43414991.105198.9
2.06-2.13.40.4415461.163199
2.1-2.143.40.31815201.195198.9
2.14-2.193.40.25215451.148199.5
2.19-2.243.40.21815351.061199
2.24-2.33.40.31915491.195199.4
2.3-2.363.40.15615291.141199.9
2.36-2.433.40.13415571.107199.8
2.43-2.513.40.11415300.972199.9
2.51-2.63.40.09315740.972199.9
2.6-2.73.50.09115511.104199.9
2.7-2.823.50.06215421.014199.9
2.82-2.973.50.05415461.0221100
2.97-3.163.50.04415671.0541100
3.16-3.43.50.03715521.016199.9
3.4-3.743.50.03315611.082199.6
3.74-4.293.40.02815551.011199.2
4.29-5.43.40.02515781.016199.4
5.4-503.20.02715121.061193.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.992→30.288 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.93
RfactorNum. reflection% reflection
Rfree0.2443 2701 10 %
Rwork0.1762 --
obs0.1831 27019 86.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.97 Å2 / Biso mean: 45.2274 Å2 / Biso min: 16.02 Å2
Refinement stepCycle: final / Resolution: 1.992→30.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 16 233 3200
Biso mean--78.22 46.79 -
Num. residues----375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093034
X-RAY DIFFRACTIONf_angle_d0.8534102
X-RAY DIFFRACTIONf_chiral_restr0.045443
X-RAY DIFFRACTIONf_plane_restr0.005533
X-RAY DIFFRACTIONf_dihedral_angle_d5.2251802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.992-2.02820.32521140.24761172128678
2.0282-2.06720.29511330.23121182131582
2.0672-2.10940.29441290.25781268139785
2.1094-2.15530.28731430.22791228137184
2.1553-2.20540.29571420.20751226136884
2.2054-2.26050.27141540.21591240139485
2.2605-2.32160.30731340.22811243137785
2.3216-2.38990.25961460.19491260140686
2.3899-2.4670.27171330.19471272140586
2.467-2.55520.28111400.18981277141786
2.5552-2.65740.28441270.19151292141987
2.6574-2.77830.24261620.18711284144688
2.7783-2.92460.26451420.19851317145988
2.9246-3.10770.28511410.1851302144389
3.1077-3.34740.27121540.17351343149790
3.3474-3.68370.24061370.16211351148890
3.6837-4.21550.21191640.14231326149091
4.2155-5.30650.18721660.13671357152392
5.3065-30.29130.22191400.17241378151889
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)
11.20590.44441.44814.5292.24912.20750.0280.2165-0.1911-0.5540.1084-0.2191-0.09890.2058-0.09180.3307-0.07280.03490.2972-0.05990.262530.8783-9.19560.516
22.80320.57990.33632.24150.57273.2521-0.0052-0.11450.08610.04120.0208-0.2540.01020.1634-0.00650.207-0.0548-0.02390.16480.01060.195936.5413-0.614916.8485
30.8126-1.18170.02974.08171.27932.2723-0.08810.4624-0.1267-0.78060.27140.2688-0.20620.1325-0.11260.3631-0.0545-0.04170.3523-0.07340.286627.2981-12.5794-4.0584
41.6565-0.56260.37211.9706-0.6995.1554-0.1776-0.27980.66280.1183-0.04130.4101-1.4268-0.6671-0.01070.70660.1347-0.12090.5849-0.12080.96290.36599.990818.417
52.1430.53141.14962.72091.06453.01290.0797-0.30860.31910.1241-0.14270.20990.0651-0.53250.05580.2799-0.08130.02230.3614-0.05440.31525.611-6.504521.5615
63.80690.1651-0.48172.9416-0.15820.79070.0935-0.0857-0.28740.0668-0.18540.02540.02410.0110.05690.2515-0.07220.01740.2706-0.01620.21757.9273-19.995815.0354
72.1241.03580.83692.9951.16942.7668-0.1445-0.22630.4799-0.3901-0.02140.3457-0.582-0.33390.12010.24980.04360.02080.4125-0.02840.36222.2201-4.262718.0055
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 2 through 21 )B2 - 21
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 65 )B22 - 65
6X-RAY DIFFRACTION6chain 'B' and (resid 66 through 114 )B66 - 114
7X-RAY DIFFRACTION7chain 'B' and (resid 115 through 188 )B115 - 188

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