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- PDB-6poi: Crystal Structure of EcDsbA in complex phenyl ether 25 -

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Basic information

Entry
Database: PDB / ID: 6poi
TitleCrystal Structure of EcDsbA in complex phenyl ether 25
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / OXIDOREDUCTASE-INHIBITOR COMPLEX / OXIDOREDUCTASE
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
COPPER (II) ION / (6-phenoxy-1-benzofuran-3-yl)acetic acid / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsIlyichova, O.V. / Scanlon, M.J.
CitationJournal: Molecules / Year: 2019
Title: The Fragment-Based Development of a Benzofuran Hit as a New Class of Escherichia coli DsbA Inhibitors.
Authors: Duncan, L.F. / Wang, G. / Ilyichova, O.V. / Scanlon, M.J. / Heras, B. / Abbott, B.M.
History
DepositionJul 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._citation.title / _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
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)42,6424
Polymers42,3102
Non-polymers3322
Water7,494416
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4232
Polymers21,1551
Non-polymers2681
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)21,2192
Polymers21,1551
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.750, 63.670, 96.600
Angle α, β, γ (deg.)90.000, 140.960, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-458-

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: B0013 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEG4
#2: Chemical ChemComp-OVS / (6-phenoxy-1-benzofuran-3-yl)acetic acid


Mass: 268.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 11-13 % PEG 8000, 5-7.5% glycerol, 100mM Na Cacodylate pH6.1, 1mM CuCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 1, 2014
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: 1.77→37.08 Å / Num. obs: 43841 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.036 / Rrim(I) all: 0.074 / Net I/σ(I): 14.1
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6376 / CC1/2: 0.77 / Rpim(I) all: 0.318 / Rrim(I) all: 0.649 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.77→34.91 Å / SU ML: 0.1902 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9506
RfactorNum. reflection% reflection
Rfree0.2064 2198 5.01 %
Rwork0.1695 --
obs0.1713 43840 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.53 Å2
Refinement stepCycle: LAST / Resolution: 1.77→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 21 416 3330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01213034
X-RAY DIFFRACTIONf_angle_d0.94164129
X-RAY DIFFRACTIONf_chiral_restr0.0561451
X-RAY DIFFRACTIONf_plane_restr0.0061543
X-RAY DIFFRACTIONf_dihedral_angle_d2.85322428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.29391280.25212628X-RAY DIFFRACTION99.75
1.81-1.850.27361370.23492527X-RAY DIFFRACTION99.78
1.85-1.90.30571330.2182597X-RAY DIFFRACTION99.82
1.9-1.950.23971430.20312591X-RAY DIFFRACTION99.74
1.95-2.010.23361410.18642584X-RAY DIFFRACTION99.89
2.01-2.070.23581470.17842585X-RAY DIFFRACTION99.74
2.07-2.140.21181420.17832585X-RAY DIFFRACTION99.74
2.14-2.230.20941410.17382601X-RAY DIFFRACTION99.82
2.23-2.330.22841420.17112586X-RAY DIFFRACTION99.82
2.33-2.450.21951670.16752582X-RAY DIFFRACTION99.75
2.45-2.610.19611440.1712572X-RAY DIFFRACTION99.74
2.61-2.810.22251390.16582617X-RAY DIFFRACTION99.75
2.81-3.090.19821110.17122633X-RAY DIFFRACTION99.71
3.09-3.540.18871310.1632636X-RAY DIFFRACTION99.71
3.54-4.460.16271160.14282649X-RAY DIFFRACTION99.64
4.46-34.910.18531360.15832669X-RAY DIFFRACTION99.36
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)
10.69240457423-0.0738409422493-0.6587681222291.28790268398-1.055485648961.527780443510.007170670076570.217531066995-0.00108286849942-0.519931354251-0.00532531183223-0.1561345926130.23939782992-0.1488610198030.0284120756130.283052812556-0.02681952427730.04896129060330.2136065122280.02335660178350.10389171702229.56977114877.68144215412-0.782282107096
27.69658058148-2.642452289374.93314597024.57009860015-2.554729123717.56714402153-0.151831618306-0.2811961334040.07493256866230.3669060879140.003764227322780.0479837622025-0.420355701168-0.1344192818320.1224799764460.159229276468-0.01507328219150.03494508407590.165789715318-0.00133098536940.13031240797627.388596656818.29555731385.59397879825
31.106249187451.20190212312-0.37880987334.79166524302-2.42415368122.82037931448-0.07712564387250.1360472627880.104244940742-0.1006625079120.2456882383660.58909237035-0.000709708210334-0.17871334332-0.1529607286570.141974443291-0.0221874387066-0.01283760038930.168957216118-0.005669658007840.10470001742122.38310176176.345838594.29759248874
42.03630039041-0.1117584974480.1392026578691.342446293180.05877409429291.54524292783-0.00925309879142-0.03713659899650.04176988150380.0937784036854-0.05223752008120.0293851647261-0.0291276161979-0.04673657335180.05935938214860.130329022522-0.03771854332180.02936314501750.1607692048170.008369820325530.052766160766523.62345449182.6590917797216.0079659313
52.201175176151.06065486851-1.191255709531.981120089870.1854681129391.70025100759-0.065454047687-0.212946599641-0.1764700077240.339832643486-0.00465141406956-0.1354992787930.04185369827820.164007428630.06733412214620.229826718073-0.06289994429140.02563657535020.2339838553490.006166472183720.056540563277227.36712021940.15932237389224.6123710753
63.066247834462.554680800761.053053308992.945607614760.6931393624533.06497928137-0.159048560143-0.2548001207070.06677415984060.2471622428380.008913542423030.49487373402-0.134259216371-0.3774458737420.1074497067150.185444600971-0.01000571134080.09161818557180.258191953895-0.02245766225590.18039598354213.4067799439-0.49646919679923.4535286934
76.25375620019-1.0093227076-3.467244828091.66587089709-0.3455319419516.10304178854-0.1718471890720.260487819094-0.282667844784-0.528924733944-0.003607854994380.3669652612850.238934549107-0.4185444100980.2012445344330.207942394049-0.061252758909-0.002090569992070.180854000851-0.0575499860930.14671455340916.4435438484-4.204196915485.13827524587
82.524919678580.2028158393772.061323250381.57836508529-1.330248900056.86691334279-0.1897173229780.38594531553-0.204830812886-0.9074610433260.2645690720310.1340957721380.51901985993-0.135239071165-0.06848969999110.333473807314-0.09254570051580.01564891940710.2627031168740.005308727213330.13050831848627.25214833835.03580840623-3.97789715427
90.96704645213-0.160169500881.082049677141.751642824730.3447337425221.37061409774-0.3555495548160.39581098123-0.0791383920633-0.5604985563780.0252388136878-0.263270165602-0.2242937858320.7017014315980.1910637534580.239543744367-0.03960580322430.06795575048990.2639184678390.02065293586470.20827041532640.201467072814.0557700296-1.86527030984
104.918377897121.193098856932.230675333763.067735759530.6160419631543.4677872511-0.05683849616830.118683718564-0.0283879870583-0.1793006424940.05799400843330.00623113724631-0.0331306176593-0.09807165672350.006166609075970.164203602598-0.01428302644370.04949157767050.147498620980.02859395705070.11150204735230.600801829917.8050752084-4.02198944137
111.047162525550.1983390120230.1184577349323.1664727935-1.613394464032.031650828110.03073489351330.13737114083-0.0246873118231-0.061310737758-0.072777260706-0.4920160198720.220763673430.2453867972320.01623495542010.1827683981040.00303393330139-0.05174205171050.1833661991020.0008423443428230.27617053072752.55391935230.99334179620522.0237890105
121.649876536060.5184717651450.3354831900052.74192072339-0.6021455156421.73394152966-0.07624738578210.101959525186-0.000179385464933-0.1791990604430.0784255664975-0.3308031184110.08184390260870.1749159377510.005161781688490.116892828992-0.02581045501850.01049594096430.177099503376-0.01296311540390.17110825961354.147999293414.574147532114.0000173402
131.274130293811.14060803899-0.3105326361924.542074086040.3780259089135.48415564512-0.000177873147314-0.02605407486580.0610824751291-0.1241393514470.0361686987155-0.06555392161170.148220838875-0.0292606694981-0.02701037619520.25136330950.000700479084867-0.1446458798910.1122964606160.0278383525040.33263329785249.3905837891-5.6087396963729.9315348214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 97 )
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 114 )
6X-RAY DIFFRACTION6chain 'A' and (resid 115 through 128 )
7X-RAY DIFFRACTION7chain 'A' and (resid 129 through 145 )
8X-RAY DIFFRACTION8chain 'A' and (resid 146 through 161 )
9X-RAY DIFFRACTION9chain 'A' and (resid 162 through 170 )
10X-RAY DIFFRACTION10chain 'A' and (resid 171 through 188 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 65 )
12X-RAY DIFFRACTION12chain 'B' and (resid 66 through 161 )
13X-RAY DIFFRACTION13chain 'B' and (resid 162 through 188 )

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