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- PDB-4wet: Crystal structure of E.Coli DsbA in complex with compound 16 -

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Basic information

Entry
Database: PDB / ID: 4wet
TitleCrystal structure of E.Coli DsbA in complex with compound 16
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-WEF / Thiol:disulfide interchange protein / :
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsIlyichova, O.V. / 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 11, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)42,8465
Polymers42,3102
Non-polymers5353
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-17 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.477, 47.118, 62.588
Angle α, β, γ (deg.)90.00, 96.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-304-

HOH

21B-390-

HOH

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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-WEF / N-({4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-thiazol-5-yl}carbonyl)-L-tyrosine


Mass: 450.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17F3N2O4S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
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 / Date: Aug 27, 2013
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: 1.63→46.42 Å / Num. obs: 43616 / % possible obs: 96.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 18.8
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.5 / % possible all: 95.4

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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: 1.63→41.681 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.04 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 2198 5.04 %Random selection
Rwork0.1766 ---
obs0.1782 43610 96.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→41.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 0 36 456 3364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063066
X-RAY DIFFRACTIONf_angle_d0.9274176
X-RAY DIFFRACTIONf_dihedral_angle_d14.3931084
X-RAY DIFFRACTIONf_chiral_restr0.034454
X-RAY DIFFRACTIONf_plane_restr0.004552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.66540.2821220.22832545X-RAY DIFFRACTION95
1.6654-1.70420.25531350.20772515X-RAY DIFFRACTION95
1.7042-1.74680.23371170.20322570X-RAY DIFFRACTION95
1.7468-1.7940.23151400.20742536X-RAY DIFFRACTION95
1.794-1.84680.26311600.2132528X-RAY DIFFRACTION96
1.8468-1.90640.28791150.21252582X-RAY DIFFRACTION96
1.9064-1.97460.25461360.20712552X-RAY DIFFRACTION96
1.9746-2.05360.22141380.19392601X-RAY DIFFRACTION96
2.0536-2.14710.23791400.18572591X-RAY DIFFRACTION97
2.1471-2.26030.21961340.18232558X-RAY DIFFRACTION96
2.2603-2.40190.2321570.18242586X-RAY DIFFRACTION97
2.4019-2.58730.21611330.18532624X-RAY DIFFRACTION97
2.5873-2.84760.21441430.17952613X-RAY DIFFRACTION97
2.8476-3.25950.19921320.18022653X-RAY DIFFRACTION98
3.2595-4.10610.19311260.14712668X-RAY DIFFRACTION98
4.1061-41.69490.15361700.14912690X-RAY DIFFRACTION97
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)
12.24760.54870.33644.79421.02622.97330.0212-0.01440.18540.08050.0075-0.143-0.18330.1942-0.0190.14590.0523-0.00210.19070.0010.156718.778528.4442-14.3143
22.9079-0.4134-0.12791.51830.44151.1148-0.03160.0150.02770.08230.0861-0.11510.01140.1845-0.04510.13120.0316-0.00450.1510.02390.104520.141820.3181-16.8789
31.38612.47592.27174.42294.06483.81020.0735-0.1066-0.32560.7081-0.1464-0.14550.25830.18350.05530.28130.0176-0.03760.13720.03460.2442-5.7724-3.8518-6.15
43.9860.1213-1.32333.4836-1.45014.14580.05630.1364-0.11510.0307-0.12760.10880.0328-0.06310.06590.12380.03160.00710.0974-0.00960.1135-7.022313.8948-12.5303
58.57320.5145-5.42074.1485-4.88158.5391-0.04410.8578-0.2893-0.80710.1760.40990.2972-0.6211-0.09310.28730.0352-0.09430.2409-0.04940.1584-10.81146.7552-22.1722
63.95041.35-0.77867.8218-0.365.02340.0611-0.0398-0.68070.0361-0.1555-0.26130.1679-0.20310.04390.12480.05410.01920.15230.02230.2156-11.155115.3898-12.5792
75.11460.07710.30262.2416-0.34832.19950.01390.13760.06530.0063-0.07330.04580.035-0.02560.05440.1030.05560.00920.10910.02970.1043-9.788924.8806-19.5366
82.789-0.27890.31592.34560.16673.6327-0.06160.27430.4157-0.0674-0.1084-0.0035-0.2777-0.03150.15820.15020.0564-0.01060.16360.06310.2219-10.805332.4708-23.1042
94.5771-3.59842.20345.3015-2.05251.5013-0.3561-0.45220.05590.63070.44170.1518-0.5266-0.6778-0.03340.23210.08440.04980.2886-0.01740.131-14.365824.8609-5.3652
103.38411.03470.87555.46931.13143.82710.19650.0798-0.5341-0.2921-0.14870.01570.4820.1333-0.04720.23470.0804-0.02590.13930.01360.1895-6.81993.3421-11.851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 188 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 11 )
4X-RAY DIFFRACTION4chain 'B' and (resid 12 through 38 )
5X-RAY DIFFRACTION5chain 'B' and (resid 39 through 49 )
6X-RAY DIFFRACTION6chain 'B' and (resid 50 through 65 )
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 97 )
8X-RAY DIFFRACTION8chain 'B' and (resid 98 through 128 )
9X-RAY DIFFRACTION9chain 'B' and (resid 129 through 144 )
10X-RAY DIFFRACTION10chain 'B' and (resid 145 through 188 )

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