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- PDB-4wf4: Crystal structure of E.Coli DsbA co-crystallised in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4wf4
TitleCrystal structure of E.Coli DsbA co-crystallised in complex with compound 4
ComponentsThiol:disulfide interchange protein
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / DSBA / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


disulfide oxidoreductase activity / periplasmic space / metal ion binding
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
Chem-WF4 / Thiol:disulfide interchange protein / :
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAdams, 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. ...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.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (Australia)1009785 Australia
CitationJournal: 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
DepositionSep 12, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 23, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.4Nov 8, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein
B: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6594
Polymers42,3102
Non-polymers3492
Water8,125451
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.183, 47.196, 62.505
Angle α, β, γ (deg.)90.00, 96.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thiol:disulfide interchange protein


Mass: 21155.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Genus: dsbA
References: UniProt: C5WBA2, UniProt: A0A0H2UL03*PLUS, protein-disulfide reductase (glutathione)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-WF4 / 4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-thiazole-5-carboxylic acid


Mass: 287.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8F3NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 100-200 mM KBr, 28-33% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD
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: 1.7→46.53 Å / Num. obs: 39824 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
Blu-Icedata collection
PHASERphasing
SCALAdata reduction
MOSFLMdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.7→36.617 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 2001 5.03 %Random selection
Rwork0.1773 ---
obs0.1787 39815 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→36.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 23 451 3355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053033
X-RAY DIFFRACTIONf_angle_d0.7924128
X-RAY DIFFRACTIONf_dihedral_angle_d14.3631072
X-RAY DIFFRACTIONf_chiral_restr0.03453
X-RAY DIFFRACTIONf_plane_restr0.004542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.29261360.22882700X-RAY DIFFRACTION100
1.7425-1.78960.26291500.22382641X-RAY DIFFRACTION100
1.7896-1.84230.30141540.23432684X-RAY DIFFRACTION100
1.8423-1.90170.31051260.22382702X-RAY DIFFRACTION100
1.9017-1.96970.26321430.20392682X-RAY DIFFRACTION100
1.9697-2.04860.24831240.19762701X-RAY DIFFRACTION100
2.0486-2.14180.20991420.18652701X-RAY DIFFRACTION100
2.1418-2.25470.24061600.18152659X-RAY DIFFRACTION100
2.2547-2.39590.20171410.18062701X-RAY DIFFRACTION100
2.3959-2.58090.19241380.18132699X-RAY DIFFRACTION100
2.5809-2.84050.18291350.1892735X-RAY DIFFRACTION100
2.8405-3.25130.24961550.1842697X-RAY DIFFRACTION100
3.2513-4.09550.1721450.15132735X-RAY DIFFRACTION100
4.0955-36.62520.14211520.14742777X-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)
11.72760.0357-0.08583.41790.02090.6370.092-0.1688-0.153-0.0256-0.0455-0.2020.09750.0995-0.03320.19-0.0672-0.00390.20050.00530.13277.5846-0.023713.0619
21.45430.1567-0.68147.87460.39344.86390.1372-0.2251-0.3876-0.0573-0.27290.04290.05390.0760.11740.141-0.08810.03230.1984-0.02690.206410.80017.270612.1358
32.86970.33220.27491.7545-0.18592.0174-0.0402-0.27160.32570.0288-0.0139-0.0681-0.107500.06440.1328-0.06160.00540.1737-0.0510.159810.063620.317421.1888
44.40963.272.32444.65212.31511.3825-0.29810.45630.0598-0.66220.4076-0.2962-0.50650.5165-0.10350.2506-0.11830.06020.32470.01330.150214.589216.43055.3572
52.9944-0.78590.49074.474-0.19542.10650.1624-0.1551-0.48520.2552-0.08990.02160.32-0.1476-0.03060.2474-0.1218-0.02810.18670.00570.18196.6357-5.096112.2485
61.71870.2482-0.01444.2239-0.85712.0528-0.00090.060.2153-0.2470.03610.1589-0.1488-0.1605-0.02460.1731-0.049-0.01660.19010.01110.163-19.023120.425414.0923
72.97670.5145-0.03341.9612-0.14421.2793-0.0565-0.00070.0418-0.13220.10580.15450.0287-0.1922-0.03450.1395-0.0383-0.01320.146-0.01270.1092-20.105111.974717.1275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 144 )
5X-RAY DIFFRACTION5chain 'A' and (resid 145 through 188 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 65 )
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 188 )

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