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- PDB-6br4: Crystal structure of Escherichia coli DsbA in complex with {N}-me... -

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Basic information

Entry
Database: PDB / ID: 6br4
TitleCrystal structure of Escherichia coli DsbA in complex with {N}-methyl-1-(3-thiophen-2-ylphenyl)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 ...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-(3-thiophen-2-ylphenyl)methanamine / COPPER (II) ION / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å
AuthorsHeras, B. / Totsika, M. / Paxman, J.J. / Wang, G. / Scanlon, M.J. / Martin, J.L.
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
Revision 1.4Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)42,6405
Polymers42,3102
Non-polymers3303
Water5,242291
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3582
Polymers21,1551
Non-polymers2031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2823
Polymers21,1551
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.224, 63.937, 74.510
Angle α, β, γ (deg.)90.000, 126.150, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

21B-431-

HOH

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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 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P0AEG4
#2: Chemical ChemComp-60L / ~{N}-methyl-1-(3-thiophen-2-ylphenyl)methanamine


Mass: 203.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NS
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.72 %
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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.99→52.84 Å / Num. obs: 29804 / % possible obs: 98 % / Redundancy: 3.67 % / Biso Wilson estimate: 34.45 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.8
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 0.261

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→52.84 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 3020 10.13 %
Rwork0.1681 26780 -
obs0.1729 29800 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.02 Å2 / Biso mean: 42.3087 Å2 / Biso min: 18.8 Å2
Refinement stepCycle: final / Resolution: 1.99→52.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 16 291 3263
Biso mean--67.9 48.39 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083037
X-RAY DIFFRACTIONf_angle_d0.8794107
X-RAY DIFFRACTIONf_chiral_restr0.045444
X-RAY DIFFRACTIONf_plane_restr0.004534
X-RAY DIFFRACTIONf_dihedral_angle_d5.2641809
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.02110.54971330.4651115124891
2.0211-2.05430.39471250.36561195132096
2.0543-2.08970.33841240.23281194131896
2.0897-2.12770.24061330.19491209134297
2.1277-2.16860.22611430.18431175131897
2.1686-2.21290.23511570.1831190134797
2.2129-2.2610.22851330.17891190132397
2.261-2.31360.2211390.16331223136298
2.3136-2.37140.2061430.15941213135698
2.3714-2.43560.22911350.16651184131998
2.4356-2.50720.26751420.1731219136198
2.5072-2.58820.2461200.17331246136699
2.5882-2.68070.23421340.18221222135698
2.6807-2.7880.24371430.16641234137799
2.788-2.91490.24731250.181227135299
2.9149-3.06850.25221400.17421230137099
3.0685-3.26070.22451440.17031235137999
3.2607-3.51250.18861380.159612401378100
3.5125-3.86580.1751310.139112621393100
3.8658-4.4250.1871560.136812331389100
4.425-5.5740.17131460.154112541400100
5.574-52.85880.18691360.16911290142699
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)
11.2127-0.47771.19628.62023.77443.26860.0170.54540.0235-1.4636-0.22570.61-0.4386-0.1719-0.00940.71370.0847-0.19840.386-0.06960.379324.6717-12.7935-13.4038
22.37462.4949-0.17943.4471.30673.9514-0.18210.97780.2815-1.32820.1334-0.4646-0.38020.89940.0090.6858-0.25830.14330.7737-0.04120.435937.6652-2.4707-9.7211
31.50141.0970.93974.33220.78072.590.12190.1677-0.1703-0.06040.0307-0.08680.14940.1704-0.15640.2808-0.044-0.02690.2939-0.01860.258430.6119-9.24275.7755
43.1816-0.10420.60780.63680.17512.5529-0.02520.1429-0.12220.01870.02070.00910.05160.0152-0.01530.2688-0.05610.00150.2342-0.03040.249434.0176-3.21915.7074
53.5790.92171.53890.9374-0.08432.6523-0.0065-0.2592-0.01070.1037-0.0060.14250.1036-0.20640.02320.2583-0.06350.00510.2563-0.02530.232630.1125-1.008624.2613
63.74822.523-0.9184.026-0.73514.1513-0.101-0.1518-0.09980.13640.0401-0.49880.08320.70920.02860.2056-0.0022-0.01820.3021-0.02880.247343.7514-0.70123.1381
73.57980.53561.49171.2740.39033.3103-0.34790.6180.1436-0.44830.3352-0.1389-0.63080.83170.04060.3665-0.15010.04440.38050.00670.292941.56523.55.1945
82.3488-0.2233-0.61795.68171.48454.75930.03830.69720.1836-1.04040.1668-0.0687-0.42250.0647-0.17170.4461-0.0852-0.0220.4427-0.02430.293130.604-4.0854-4.6736
93.03845.0563-2.99198.3162-4.62793.7780.1270.48680.151-0.71050.18481.73040.0373-0.9023-0.16430.46240.063-0.16140.3402-0.00520.783817.744-14.2345-2.6616
103.2125-0.028-1.03725.76250.65634.22080.03040.269-0.1676-0.5781-0.05890.36890.12630.1064-0.11610.34010.064-0.1240.3438-0.1160.367727.7691-17.9904-4.2791
112.34551.4742-0.35942.07490.68232.15240.06690.28310.5251-0.44410.27890.3164-1.5143-0.6831-0.1880.76310.19020.17970.43430.06630.60991.57810.055220.1484
121.05150.31860.43892.60652.33174.34770.0798-0.03890.08850.1193-0.09520.207-0.0618-0.3715-0.09310.3083-0.0430.02180.25840.01330.35775.8871-6.607921.8556
136.22530.0712-1.84543.46820.74953.94210.17250.5321-0.0035-0.3226-0.05340.11980.1313-0.4903-0.11280.2545-0.024-0.04510.2643-0.02140.21863.1574-16.441610.9301
144.29871.0315-2.31732.5274-0.51381.80610.0174-0.2708-0.47280.2059-0.1426-0.26140.04680.17940.1350.2929-0.0526-0.00720.3031-0.00150.300510.4107-21.803216.6879
155.20550.18831.77714.0353-0.4895.2361-0.21990.3068-0.5782-0.21660.07520.22750.4181-0.43990.12080.2642-0.10640.02460.4553-0.00640.3239-1.6242-27.137412.1545
162.03272.4019-1.06549.332-1.98222.3986-0.08640.50140.5129-0.49130.33531.2442-0.3391-0.774-0.10920.2960.0738-0.07450.50320.09180.3534-4.4743-9.56758.3141
175.0366-1.98040.49355.16971.61716.11050.49290.24181.0054-0.6398-0.0740.3854-1.676-0.6109-0.39170.60160.10430.13820.34120.07630.51913.2793.306615.7372
183.3189-0.7378-0.85265.9019-4.53384.0706-0.1822-0.1340.0154-0.7281-0.1403-0.837-0.10890.85990.26130.6681-0.06590.32010.3848-0.06240.633715.05556.062126.5212
194.08821.39351.13413.3321-0.07345.91990.4736-0.06960.80710.0201-0.14550.1466-0.4911-0.375-0.22640.4830.01950.21940.2239-0.0410.48475.27664.558129.9144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )A1 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 21 )A12 - 21
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 65 )A22 - 65
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 97 )A66 - 97
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 114 )A98 - 114
6X-RAY DIFFRACTION6chain 'A' and (resid 115 through 128 )A115 - 128
7X-RAY DIFFRACTION7chain 'A' and (resid 129 through 145 )A129 - 145
8X-RAY DIFFRACTION8chain 'A' and (resid 146 through 161 )A146 - 161
9X-RAY DIFFRACTION9chain 'A' and (resid 162 through 170 )A162 - 170
10X-RAY DIFFRACTION10chain 'A' and (resid 171 through 188 )A171 - 188
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 21 )B1 - 21
12X-RAY DIFFRACTION12chain 'B' and (resid 22 through 65 )B22 - 65
13X-RAY DIFFRACTION13chain 'B' and (resid 66 through 82 )B66 - 82
14X-RAY DIFFRACTION14chain 'B' and (resid 83 through 114 )B83 - 114
15X-RAY DIFFRACTION15chain 'B' and (resid 115 through 128 )B115 - 128
16X-RAY DIFFRACTION16chain 'B' and (resid 129 through 144 )B129 - 144
17X-RAY DIFFRACTION17chain 'B' and (resid 145 through 161 )B145 - 161
18X-RAY DIFFRACTION18chain 'B' and (resid 162 through 170 )B162 - 170
19X-RAY DIFFRACTION19chain 'B' and (resid 171 through 188 )B171 - 188

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