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- PDB-4wf5: Crystal structure of E.Coli DsbA soaked with compound 4 -

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Basic information

Entry
Database: PDB / ID: 4wf5
TitleCrystal structure of E.Coli DsbA soaked 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
COPPER (II) ION / Chem-WF4 / Thiol:disulfide interchange protein / :
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)43,1027
Polymers42,3102
Non-polymers7925
Water8,269459
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.246, 63.401, 74.402
Angle α, β, γ (deg.)90.00, 126.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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)

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Non-polymers , 5 types, 464 molecules

#2: Chemical ChemComp-WF4 / 4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-thiazole-5-carboxylic acid


Mass: 287.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H8F3NO2S
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.65 Å3/Da / Density meas: 53.55 Mg/m3 / Density % sol: 54.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
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: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 18, 2012
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: 1.45→37.16 Å / Num. obs: 78184 / % possible obs: 99.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.7
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.3 / % possible all: 97.8

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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: 1.45→34.46 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 3936 5.03 %
Rwork0.1602 --
obs0.162 78182 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→34.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 49 459 3412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073129
X-RAY DIFFRACTIONf_angle_d0.9624258
X-RAY DIFFRACTIONf_dihedral_angle_d14.2531137
X-RAY DIFFRACTIONf_chiral_restr0.039457
X-RAY DIFFRACTIONf_plane_restr0.005558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46770.2421310.22872583X-RAY DIFFRACTION97
1.4677-1.48630.2811390.21992580X-RAY DIFFRACTION98
1.4863-1.50580.26111500.20522565X-RAY DIFFRACTION98
1.5058-1.52640.22851460.20212637X-RAY DIFFRACTION98
1.5264-1.54830.25521370.18352623X-RAY DIFFRACTION99
1.5483-1.57140.22881370.1732594X-RAY DIFFRACTION99
1.5714-1.59590.20431270.17092685X-RAY DIFFRACTION99
1.5959-1.62210.21211340.162650X-RAY DIFFRACTION100
1.6221-1.65010.20191330.1612642X-RAY DIFFRACTION100
1.6501-1.68010.20061550.15612641X-RAY DIFFRACTION100
1.6801-1.71240.18941360.15012652X-RAY DIFFRACTION100
1.7124-1.74730.22721520.15062628X-RAY DIFFRACTION100
1.7473-1.78530.19941490.1492654X-RAY DIFFRACTION100
1.7853-1.82680.19971490.1512640X-RAY DIFFRACTION100
1.8268-1.87250.22081470.16052682X-RAY DIFFRACTION100
1.8725-1.92310.23251470.16692648X-RAY DIFFRACTION100
1.9231-1.97970.19571330.15922662X-RAY DIFFRACTION100
1.9797-2.04360.16841490.15392675X-RAY DIFFRACTION100
2.0436-2.11670.1981340.15352663X-RAY DIFFRACTION100
2.1167-2.20140.18291420.1462637X-RAY DIFFRACTION100
2.2014-2.30160.20221180.15582695X-RAY DIFFRACTION100
2.3016-2.42290.20441210.15462695X-RAY DIFFRACTION100
2.4229-2.57460.2021420.1612702X-RAY DIFFRACTION100
2.5746-2.77330.21411440.15792665X-RAY DIFFRACTION100
2.7733-3.05230.20781390.15822696X-RAY DIFFRACTION100
3.0523-3.49360.17111350.16242684X-RAY DIFFRACTION100
3.4936-4.40010.15171480.14622691X-RAY DIFFRACTION100
4.4001-34.470.19651620.17022677X-RAY DIFFRACTION98

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