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- PDB-8cxe: Crystal Structure of EcDsbA in a complex with 1H-imidazole -

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Basic information

Entry
Database: PDB / ID: 8cxe
TitleCrystal Structure of EcDsbA in a complex with 1H-imidazole
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / Microfrag screening / FBDD / Fragment
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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
IMIDAZOLE / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsWhitehouse, R.L. / Ilyichova, O.V. / Taylor, A.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)IC180100021 Australia
Australian Research Council (ARC)DP200100796 Australia
CitationJournal: Rsc Med Chem / Year: 2023
Title: Fragment screening libraries for the identification of protein hot spots and their minimal binding pharmacophores.
Authors: Whitehouse, R.L. / Alwan, W.S. / Ilyichova, O.V. / Taylor, A.J. / Chandrashekaran, I.R. / Mohanty, B. / Doak, B.C. / Scanlon, M.J.
History
DepositionMay 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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)42,93211
Polymers42,3102
Non-polymers6229
Water8,449469
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5006
Polymers21,1551
Non-polymers3455
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)21,4315
Polymers21,1551
Non-polymers2764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.825, 64.822, 75.075
Angle α, β, γ (deg.)90.000, 125.752, 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

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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 K-12 (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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
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: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.47→49 Å / Num. obs: 76352 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.76 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.025 / Rrim(I) all: 0.048 / Χ2: 0.52 / Net I/σ(I): 15.8
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 345 / CC1/2: 0.735 / Rpim(I) all: 0.876 / Rrim(I) all: 0.738 / Χ2: 0.43 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.19-4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.47→33.08 Å / SU ML: 0.1529 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.6994
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2029 960 1.26 %
Rwork0.174 75242 -
obs0.1743 76202 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.48 Å2
Refinement stepCycle: LAST / Resolution: 1.47→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 45 472 3407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00593064
X-RAY DIFFRACTIONf_angle_d0.79754154
X-RAY DIFFRACTIONf_chiral_restr0.0733453
X-RAY DIFFRACTIONf_plane_restr0.005591
X-RAY DIFFRACTIONf_dihedral_angle_d4.3774460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.550.25721280.24110466X-RAY DIFFRACTION97.43
1.55-1.640.22441570.20310666X-RAY DIFFRACTION99.8
1.64-1.770.21211450.188610777X-RAY DIFFRACTION99.91
1.77-1.950.24261250.173810828X-RAY DIFFRACTION99.95
1.95-2.230.19641360.168810770X-RAY DIFFRACTION99.86
2.23-2.810.23451400.181510795X-RAY DIFFRACTION99.62
2.81-33.080.17371290.16110940X-RAY DIFFRACTION99.6
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)
10.7526525937670.2028752358470.9010809236882.477442604651.42072396261.64935689985-0.01865882514850.180058767464-0.0615072865501-0.4106045952180.03040273005750.0067157441747-0.1322329957230.1199384252810.002223779935460.240198780158-0.02491143459370.003553172977220.202029512341-0.01886095730990.16779414668329.2538609919-1.7713491033-1.33250937005
20.3458155647540.7079818820430.393410531772.467717341841.063023459111.047097140880.03663443446060.0486678678446-0.1213852404140.1428180601350.109752171921-0.3275906132560.1516687305720.0497682881082-0.1164770686370.157109773909-0.00757241228288-0.005977959418550.168194590385-0.01229552017840.20383916384633.2524567722-5.570115426065.23385662641
31.643007956240.56152499958-0.1822725620241.762269098020.2946306532141.642053811090.0157685504309-0.06813951903420.008953137335090.0734220289022-0.0339783981953-0.082210499105-0.009947241287230.03341284187680.01828857005990.121903939373-0.023673379465-0.0127558396370.1228947534110.009119141479910.1124247329236.38449657816.1373569486517.0584259447
40.9705720284940.5926179972790.5328859826722.119002901951.199554671331.38603438936-0.1539754209810.200044945481-0.0189022539256-0.2896968020070.17046784417-0.0607500638206-0.1077702636960.111840974639-0.02452103753730.204417580292-0.024061734240.007487057040070.176897078251-0.005465305330860.18317793487926.6839262195-7.03392066981-3.63903318811
50.9316116259070.584575024429-0.06062594835361.37440922610.7356960758311.82614113657-0.06490970447550.04299183194610.13621616077-0.0685161973328-0.0390581819320.199532502187-0.267916951031-0.03650330279150.08956409943050.198518238593-0.00903192949746-0.01784398550290.166309537818-0.001687568169760.1779360138925.427896711337.4456335020419.5903114777
63.58580212749-1.03386806335-0.8325035153291.787565395890.3063390843741.59184565233-0.178209719994-0.170580455222-0.2259584142650.09450533140340.02843221878240.2121272482820.1567595299450.001708078955090.1343365425690.1889399341840.002400008398820.02869345384060.1751824870170.003954717876560.1994854769466.145326227421.9344599766530.5546959176
71.67802446370.2981525915280.4760715579541.834185944020.5231424643521.629702489530.044750778546-0.0822353337950.1210798354320.0235863889501-0.05761596225130.1284716038860.0910324446084-0.05329633333360.004187458829550.150483504644-0.0120280244739-0.003620049891530.150779177793-0.01322706231360.15506177934.44284229006-6.861927525716.5410402223
81.477267083670.359338139264-0.6409463111341.30231171525-0.5321084960921.27613563496-0.101769886382-0.00867104440073-0.272293454594-0.1046782924440.044194403617-0.1720536060960.140591566488-0.01326840889560.04476875037920.155892264666-0.007025092306770.01274423026670.166800646025-0.01695334004910.1731671724746.44511056963-19.04651799113.4688681206
91.198014593091.194254913720.05554634636015.1057089485-0.3386747953891.22331342232-0.178519396933-0.01513585243440.282823222103-0.3385071650030.1619633813470.647409453571-0.171104503805-0.3330491435590.02828904235990.1984881166350.0184677075438-0.0708694022240.2245678100140.009368487183720.228973303713-4.13552967942-2.763114505698.16304716775
102.73232164807-0.807877539807-0.3407575737272.540998777670.7561378691052.25018253496-0.0447568215046-0.04519894803940.237152634301-0.28395923641-0.08448183745510.198683854894-0.393062208683-0.224314195930.1098431893660.2305668223010.0203622460231-0.04712057848320.191805466771-0.008904271820950.220517854542.475767722299.6560298593716.1789835092
111.411662117620.5117852162190.2597851043781.93643512208-0.05695284088952.73227886537-0.0773597242696-0.08817929488730.18154925515-0.0191087167538-0.05725644438820.0455566476833-0.250456093840.04308505621820.1301597206230.211474132050.01019941660460.01052095098740.163353554377-0.0162541052630.2072215881437.2504447456912.221162839728.6592802627
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 38 )AA1 - 381 - 38
22chain 'A' and (resid 39 through 65 )AA39 - 6539 - 65
33chain 'A' and (resid 66 through 145 )AA66 - 14566 - 145
44chain 'A' and (resid 146 through 188 )AA146 - 188146 - 188
55chain 'B' and (resid 1 through 38 )BG1 - 381 - 38
66chain 'B' and (resid 39 through 49 )BG39 - 4939 - 49
77chain 'B' and (resid 50 through 97 )BG50 - 9750 - 97
88chain 'B' and (resid 98 through 128 )BG98 - 12898 - 128
99chain 'B' and (resid 129 through 145 )BG129 - 145129 - 145
1010chain 'B' and (resid 146 through 161 )BG146 - 161146 - 161
1111chain 'B' and (resid 162 through 188 )BG162 - 188162 - 188

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