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- PDB-8d10: Crystal Structure of EcDsbA in a complex with (1-methyl-1H-pyrazo... -

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Basic information

Entry
Database: PDB / ID: 8d10
TitleCrystal Structure of EcDsbA in a complex with (1-methyl-1H-pyrazol-5-yl)methanamine
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 / 1-(1-methyl-1H-pyrazol-5-yl)methanamine / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 26, 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 6, 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)42,7076
Polymers42,3102
Non-polymers3974
Water7,044391
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2662
Polymers21,1551
Non-polymers1111
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)21,4414
Polymers21,1551
Non-polymers2863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.560, 65.082, 74.938
Angle α, β, γ (deg.)90.000, 126.282, 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 1 through 7 or resid 9...
d_2ens_1(chain "B" and (resid 1 through 6 or (resid 7...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALALYSA1 - 7
d_12ens_1TYRLEUA9 - 23
d_13ens_1PHEGLUA25 - 37
d_14ens_1VALGLNA39 - 97
d_15ens_1THRALAA99 - 105
d_16ens_1ASPILEA107 - 113
d_17ens_1ALALYSA115 - 132
d_18ens_1LEULYSA134 - 188
d_21ens_1ALALYSC1 - 7
d_22ens_1TYRLEUC9 - 23
d_23ens_1PHEGLUC25 - 37
d_24ens_1VALGLNC39 - 97
d_25ens_1THRALAC99 - 105
d_26ens_1ASPILEC107 - 113
d_27ens_1ALALYSC115 - 132
d_28ens_1LEULYSC134 - 188

NCS oper: (Code: givenMatrix: (-0.949469615779, 0.0736743204542, 0.30508940201), (-0.310369110542, -0.0758424432083, -0.947585847842), (-0.0466740177663, -0.994394297205, 0.0948763287219)Vector: 32. ...NCS oper: (Code: given
Matrix: (-0.949469615779, 0.0736743204542, 0.30508940201), (-0.310369110542, -0.0758424432083, -0.947585847842), (-0.0466740177663, -0.994394297205, 0.0948763287219)
Vector: 32.5143957184, 14.5325044828, 18.8478530828)

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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-Q2I / 1-(1-methyl-1H-pyrazol-5-yl)methanamine


Mass: 111.145 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C5H9N3 / 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.: 391 / 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: 54.88 %
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: 0.95365 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: 0.95365 Å / Relative weight: 1
ReflectionResolution: 1.47→49.09 Å / Num. obs: 75786 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 22.21 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.028 / Rrim(I) all: 0.053 / Χ2: 0.51 / Net I/σ(I): 13.1
Reflection shellResolution: 1.47→1.49 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.057 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3343 / CC1/2: 0.557 / Rpim(I) all: 0.66 / Rrim(I) all: 0.661 / Χ2: 0.37 / % possible all: 88.7

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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: 1.6→34.59 Å / SU ML: 0.1117 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.0903
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1976 759 1.28 %
Rwork0.1805 58350 -
obs0.1807 59109 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.52 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 25 392 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813022
X-RAY DIFFRACTIONf_angle_d0.97824110
X-RAY DIFFRACTIONf_chiral_restr0.058449
X-RAY DIFFRACTIONf_plane_restr0.0067564
X-RAY DIFFRACTIONf_dihedral_angle_d4.534431
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.11325945546 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.720.24321610.203611592X-RAY DIFFRACTION100
1.72-1.90.24261390.200511673X-RAY DIFFRACTION100
1.9-2.170.20981450.188911607X-RAY DIFFRACTION99.97
2.17-2.740.23281570.192611669X-RAY DIFFRACTION99.92
2.74-34.590.16991570.167311809X-RAY DIFFRACTION99.77
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)
10.7027292260690.2434795229590.9469099599044.268145470712.248349313051.984172662520.01342039149910.1806604354-0.0938701590071-0.3754005314220.0847993258139-0.0904815235294-0.02105817921490.0332793261195-0.05548135769260.208092557882-0.04373163420610.02507813880690.193225699618-0.01602124056830.15515934882630.2325998668-3.167919248021.01855764732
22.686338494170.7955259906370.2761770159212.123919497470.7393874688962.39234058470.0128862014547-0.0820751699918-0.007030228308910.105282204958-4.01950969885E-5-0.154027546760.07191952160330.0115481512442-0.01401258915050.144533878148-0.0157308714558-0.01329674808160.1322506696290.006159252546290.13907570934735.73447138135.4500918730316.799853188
31.300295094960.2638942563940.6571970330035.151530666291.823325400312.77978671005-0.0446071757170.220686636925-0.102375492093-0.5021800409420.142142866040.198609683282-0.0321642670460.162677166963-0.1005042186170.231225697907-0.0310810929585-0.02415080067310.230310804981-0.02763402791280.19295633198926.7810197709-7.00360352312-3.82322248718
41.445606506790.896250826024-0.9349091251453.5942205977-0.347768987843.161510919980.1929610057860.1314549684830.2603517629170.0117316479246-0.1872406682380.653766198412-0.876086189348-0.722843777148-0.004854437981650.4899111480850.122660947346-0.05402589009370.2930961129270.00190375645770.3474417901920.05624383268715.803852924420.0582454286
51.65631424554-0.8524804930070.1071948353972.391441603621.184774035933.53398048431-0.00174870824895-0.011599706885-0.0604444572097-0.00905597666286-0.01467488590830.1748698727080.10978080108-0.03046514140240.03440292953580.164747963304-0.02528209726920.01371978986650.151709114921-0.01711295801450.1972494936068.26132805683-0.78064063352323.1798413797
62.89709261912-0.01265267136950.08529465705554.205208664211.072287069931.40307552204-0.005294722878770.01242131651070.0128067434941-0.140151113142-0.0447834030136-0.01077878653240.0138057513032-0.04429757066960.04276624700380.158369904868-0.0100283874508-0.01778014783230.162091546109-0.0127942341080.1196119462866.46886840316-10.851133024715.6778757862
70.6566682572360.7079772787360.3321454550642.947825346731.018387136581.85082035549-0.1037167813230.006575957502010.136259502555-0.387891218097-0.02592621112390.337190946658-0.352668956619-0.182786227130.1403019417850.14921840320.0362498183403-0.02083794384650.2107760394920.001935946334520.2083154783361.791196333391.6238789204618.3442929731
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 65 )AA1 - 651 - 65
22chain 'A' and (resid 66 through 145 )AA66 - 14566 - 145
33chain 'A' and (resid 146 through 188 )AA146 - 188146 - 188
44chain 'B' and (resid 1 through 21 )BC1 - 211 - 21
55chain 'B' and (resid 22 through 49 )BC22 - 4922 - 49
66chain 'B' and (resid 50 through 114 )BC50 - 11450 - 114
77chain 'B' and (resid 115 through 188 )BC115 - 188115 - 188

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