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- PDB-8dg0: Crystal Structure of EcDsbA in a complex with Urea -

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Basic information

Entry
Database: PDB / ID: 8dg0
TitleCrystal Structure of EcDsbA in a complex with Urea
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / Microfrag screening / FBDD / Fragment / ANTIMICROBIAL PROTEIN
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
COPPER (II) ION / UREA / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionJun 23, 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 1.3Nov 13, 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

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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)42,7379
Polymers42,3102
Non-polymers4277
Water45025
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3955
Polymers21,1551
Non-polymers2404
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)21,3424
Polymers21,1551
Non-polymers1873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.341, 64.324, 75.346
Angle α, β, γ (deg.)90.000, 125.318, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 7 through 15 or (resid 16...
d_2ens_1(chain "B" and (resid 7 through 20 or (resid 21...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSLYSA1 - 182
d_12ens_1UREURED
d_21ens_1LYSLYSF6 - 187
d_22ens_1UREUREI

NCS oper: (Code: givenMatrix: (-0.95984303869, 0.0653676849272, 0.272815701244), (-0.276936482067, -0.0654642513176, -0.95865562988), (-0.044805423538, -0.995711553396, 0.0809381026149)Vector: 34. ...NCS oper: (Code: given
Matrix: (-0.95984303869, 0.0653676849272, 0.272815701244), (-0.276936482067, -0.0654642513176, -0.95865562988), (-0.044805423538, -0.995711553396, 0.0809381026149)
Vector: 34.4126107497, 8.70136348014, 14.0526942913)

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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-URE / UREA


Mass: 60.055 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH4N2O / Feature type: SUBJECT OF INVESTIGATION
#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.: 25 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
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: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.4→48.85 Å / Num. obs: 17916 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 47.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.061 / Rrim(I) all: 0.117 / Χ2: 0.98 / Net I/σ(I): 13.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.497 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1847 / CC1/2: 0.8 / Rpim(I) all: 0.869 / Χ2: 0.99 / % possible all: 100

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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: 2.5→47.46 Å / SU ML: 0.4051 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3869
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2573 807 5.09 %
Rwork0.2024 15053 -
obs0.2051 15860 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.44 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 0 22 26 2819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792849
X-RAY DIFFRACTIONf_angle_d0.92563876
X-RAY DIFFRACTIONf_chiral_restr0.0524437
X-RAY DIFFRACTIONf_plane_restr0.0072509
X-RAY DIFFRACTIONf_dihedral_angle_d4.1683385
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.93449717038 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.660.34261200.29322513X-RAY DIFFRACTION99.92
2.66-2.860.34781440.27112463X-RAY DIFFRACTION99.92
2.86-3.150.29761670.2572474X-RAY DIFFRACTION99.85
3.15-3.610.2894940.23372525X-RAY DIFFRACTION99.89
3.61-4.540.24361320.17092521X-RAY DIFFRACTION100
4.54-47.460.20481500.15952557X-RAY DIFFRACTION99.89
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)
16.56042413164-0.2422414251452.276438494825.87653991511-0.8336680571666.95536932929-0.5183126003120.369649849644-0.540752609087-2.266068200370.55705401968-1.20625434618-0.9481142840550.734112636056-0.003382951270931.13455201304-0.2615433977010.2138182291280.724725161852-0.166210673580.69227473756833.669294202-5.61231400634-9.36592002583
21.665078652821.177935630690.9753189781764.105223129341.025230984143.003357077460.119168705158-0.288910222287-0.09455372938560.120732378253-0.00881832966696-0.2268263303220.30376013908-0.0484522081373-0.1001458252310.463450020823-0.0676066076433-0.001747549896860.400807708375-0.04962140347720.43731174908729.8466618628-10.86006639046.79505973642
32.343167890310.4096310578930.2588907244931.23686552737-0.2432669121823.69841804810.01162649062570.0006200098135050.165928598285-0.0593545267554-0.0229662790037-0.057590860457-0.1595136023850.1616212555940.02040022515570.34267624426-0.0380891429402-0.0002000475331360.241695729369-0.03298280787840.34593169659136.2199751170.081156449015616.1442161221
42.228763041441.83601320514-0.2346800107924.737972028570.9563521002782.70613050176-0.3564824125010.381737394819-0.445671122349-1.002621178260.233025206739-0.1304515622590.209490192040.0637767023490.07392597483580.671619495864-0.06209416274660.01398527039870.529701370859-0.06214011522780.50286479606927.3085001956-12.1872925561-3.28179175276
50.8341240366070.4909315893780.5163121770320.5089830844560.793309993633.63813037303-0.7518190771790.3047753214340.837006158243-0.295481169252-0.6298370266180.178307898758-2.37687203622-0.5404869775611.191370368071.404344742380.2664844937150.2525921769230.6320805939460.1569068826991.340123102125.4562654558813.775021232623.8346910409
63.400851170871.716118395160.2641043716642.983625695070.5154495487610.4898963128640.3448968573370.5461173553211.07850031581-0.244698177357-0.3324153747020.869946310371-0.662984230686-0.6556106161180.04257906098390.9201030192950.400172948460.01888160671741.129173586460.01547877130520.818447331183-5.194957939645.6594379485214.8233792949
72.897679223141.542525876310.6911586937632.875895503690.4457004659084.536629646370.171583816469-0.0315057666127-0.131505963240.268489055575-0.08326855998410.074409423386-0.314948792119-0.418888705039-0.07994441708420.422929316722-0.04052033102350.02627205731270.4563224841850.02592146801620.41852367481110.3004101077-6.7099095033919.4539220361
85.995427376561.76755623094-0.9372520987942.99562599266-0.2541103233472.724471614120.310800853296-0.763209431114-0.3672610275810.616686359311-0.1819660991691.045792276210.227975993919-0.3981144912790.027139024170.491856704813-0.03952822921190.1456102488540.504320537661-0.05587305120690.5405133262286.11176662594-4.182979526431.1118837915
91.597753073410.41625759841.810372146555.808953017582.48158670962.74941678321-0.0249692870459-0.2286036905490.3622143402610.0384316374371-0.3730779044250.4439294425440.0066309824083-0.5384188953820.4640579122610.422550423042-0.0213126184264-0.06290795137730.565910070652-0.002515010856680.5155299091122.00477937527-5.6537899831518.181210491
103.341881639061.72397452778-2.004935130654.05815031815-0.9086678085453.0846693485-0.02662851472530.314029268199-0.340114409268-0.0434581770864-0.08689330689030.07133794756190.0738015373273-0.3116647414860.1534129863290.330860661505-0.05233045657160.01461625889070.4315029485210.01237604276850.2927291755424.15714082912-18.055981910413.7163715676
111.224226036090.748362494215-0.1814511153913.04269454630.7017525770515.56709491412-0.0358555927075-0.2310558337650.8695997684010.005942205791030.1342479073650.263047753296-1.43203404487-0.828309264263-0.02137096602380.7416713112040.1350589075810.1964062854330.5158547844290.03092041759340.800110514597.339127462385.2162990220720.7082866058
122.548214638491.517525480740.5598588162262.885899464170.214438209044.946035296530.537279116506-0.01756532064391.028296084650.174060331254-0.3246539629790.0946962930192-0.88955584268-0.782737737746-0.2609295908220.7056328350220.1547260635740.2250272893810.620300936098-0.1197633968450.7571722519245.253924178555.6348230393630.2769572519
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 21 )AA7 - 211 - 15
22chain 'A' and (resid 22 through 55 )AA22 - 5516 - 49
33chain 'A' and (resid 56 through 144 )AA56 - 14450 - 138
44chain 'A' and (resid 145 through 188 )AA145 - 188139 - 182
55chain 'B' and (resid 2 through 11 )BF2 - 111 - 10
66chain 'B' and (resid 12 through 21 )BF12 - 2111 - 20
77chain 'B' and (resid 22 through 38 )BF22 - 3821 - 37
88chain 'B' and (resid 39 through 49 )BF39 - 4938 - 48
99chain 'B' and (resid 50 through 66 )BF50 - 6649 - 65
1010chain 'B' and (resid 67 through 145 )BF67 - 14566 - 144
1111chain 'B' and (resid 146 through 170 )BF146 - 170145 - 169
1212chain 'B' and (resid 171 through 188 )BF171 - 188170 - 187

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