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- PDB-6pmf: Crystal Structure of EcDsbA in complex with aniline 15 -

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Basic information

Entry
Database: PDB / ID: 6pmf
TitleCrystal Structure of EcDsbA in complex with aniline 15
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-(phenylamino)-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: 1.95 Å
AuthorsIlyichova, O.V. / Scanlon, M.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
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 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 7, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Oct 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 1.4Nov 20, 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)42,6414
Polymers42,3102
Non-polymers3312
Water4,810267
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4222
Polymers21,1551
Non-polymers2671
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)117.720, 64.070, 74.730
Angle α, β, γ (deg.)90.000, 125.530, 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-418-

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-LD9 / [6-(phenylamino)-1-benzofuran-3-yl]acetic acid


Mass: 267.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
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: Aug 14, 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: 1.95→57.05 Å / Num. obs: 33087 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 29.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.036 / Rrim(I) all: 0.073 / Net I/σ(I): 12.8
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.586 / Num. unique obs: 4802 / CC1/2: 0.884 / Rpim(I) all: 0.329 / Rrim(I) all: 0.673 / % possible all: 99.9

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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: 1.95→37.28 Å / SU ML: 0.2505 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.724
RfactorNum. reflection% reflection
Rfree0.2268 1652 5 %
Rwork0.1909 --
obs0.1927 33049 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.81 Å2
Refinement stepCycle: LAST / Resolution: 1.95→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 21 267 3158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392989
X-RAY DIFFRACTIONf_angle_d0.57174067
X-RAY DIFFRACTIONf_chiral_restr0.0392449
X-RAY DIFFRACTIONf_plane_restr0.0036532
X-RAY DIFFRACTIONf_dihedral_angle_d2.95372387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.36741360.31082599X-RAY DIFFRACTION99.45
2.01-2.070.32641650.2772562X-RAY DIFFRACTION99.74
2.07-2.150.3261330.24842604X-RAY DIFFRACTION99.74
2.15-2.230.29521590.23112572X-RAY DIFFRACTION99.64
2.23-2.330.2911180.22272618X-RAY DIFFRACTION99.71
2.33-2.460.23571020.2122658X-RAY DIFFRACTION99.57
2.46-2.610.23071110.21972630X-RAY DIFFRACTION99.93
2.61-2.810.26761200.20262644X-RAY DIFFRACTION99.86
2.81-3.10.25911450.20542589X-RAY DIFFRACTION99.78
3.1-3.540.19861430.18452631X-RAY DIFFRACTION99.89
3.54-4.460.17951590.15062611X-RAY DIFFRACTION99.82
4.46-37.280.18961610.15492679X-RAY DIFFRACTION99.86
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)
11.096644417190.3005822321.197967216013.917794350722.605124208782.580818436160.09378229258360.0781911431759-0.040580228184-0.150900983720.001590883101050.0477641049543-0.01386117119720.102509950883-0.05201567114250.29320506412-0.06970394781120.004896441647730.313799741603-0.02757097971440.24704983225431.2196651162-9.715700509251.19087801972
21.887320330580.3077472306490.2428449181131.970626163040.07142938758962.82657386826-0.122920454373-0.0437084900590.103851872336-0.06334638450510.0566575518789-0.128532081690.120527926710.2255298525370.05370347246060.212505135897-0.02489819111440.00191543291790.252730887504-0.004537140756860.19828693303737.2614798014-0.74140199661816.7172221902
32.62309128721.28859048355-0.8559852745173.709088260620.5240004638223.215444858030.08580826359740.06553409048910.103510560812-0.2682099045530.001008148822260.271681439545-0.1216312439440.254947710885-0.1238653965270.2565667288170.000449122183661-0.04450646911570.251511684903-0.03261726115570.21894209833427.3905170666-13.3639351294-3.65146953544
41.088573145421.19248100593-0.3149153087652.925497014211.164450845941.445299047410.3328176453690.04348450642130.578635103135-0.196420301264-0.1368661890830.310644426778-0.657018329816-0.392312587605-0.175623886130.4858045075920.1037966719290.129870084410.3116016525580.03907552124890.4081345647916.86340990010.90239969197220.6240434723
56.52404262223-1.78874664471-2.783692842462.30657093671.933573347493.423843111750.182291436053-0.252701879792-0.3321745070390.233028071978-0.2206138330490.7756229863980.220801101032-0.04493112256480.09273449073540.393361287578-0.00890924953310.1754334592230.19512801067-0.01436388362050.4524581589587.46720762421-5.5940305068731.2214645235
63.26899779833-0.065865348012.060058680046.800935301171.108572341581.491369321950.346753201291-0.01066219561990.750195929501-0.205589705123-0.2992038331680.340394796217-0.269990259519-0.513359079145-0.04580680934170.3839250084130.08932377653440.04382940498560.3963780693490.05406800007680.4500755979172.31229661855-6.7847403379418.8475335016
73.686686937570.758066373302-1.801277553782.656492808310.5721195721422.4297929996-0.2751532062160.0291002883009-0.438017341538-0.1432905535890.00436881084393-0.04214575959970.118003257279-0.143541396680.2708653429110.225596005314-0.003341172273120.009852828509810.2548338577380.01897095974640.2443221479166.47762038629-21.879273671614.5248312018
82.804487642360.1089443729840.001896167592640.109656887365-0.5451838862882.725353313360.3199909264950.4180842974210.900096723625-0.3407404151360.07637740655670.582543346835-0.994054578112-0.630290203164-0.06482166285760.551763713580.2870604193230.03566129601930.5655415945430.2010453565620.5084045214570.643486146604-2.7125164691513.1890259167
91.29614459454-2.230648000521.022004998478.78292205871-8.113479774318.97094689656-0.1855030237040.03403307958260.522701858914-0.342446052823-0.326346197642-0.763010351149-0.6388249058230.8731604063390.4575548578230.744377328855-0.1121156419210.3625057332540.343414514798-0.0900677895120.66240202048616.09876720465.7843123105327.0876426107
100.8166030870231.494954804120.3201525904282.728231635850.6244965614635.837805408970.3882685736760.04902009299730.8754510140890.0823976421466-0.2784387417330.233161944588-0.340290603569-0.4946028354820.00684822319050.5702845510940.05263002654980.3012777725270.2734567053260.005667780707770.6109083936436.34117488314.2453841886730.7270818929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 145 )
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 188 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 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 128 )
8X-RAY DIFFRACTION8chain 'B' and (resid 129 through 161 )
9X-RAY DIFFRACTION9chain 'B' and (resid 162 through 170 )
10X-RAY DIFFRACTION10chain 'B' and (resid 171 through 188 )

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