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- PDB-8d12: Crystal Structure of EcDsbA in a complex with 1-methyl-1H-pyrazol... -

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Basic information

Entry
Database: PDB / ID: 8d12
TitleCrystal Structure of EcDsbA in a complex with 1-methyl-1H-pyrazol-4-amine
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-methyl-1H-pyrazol-4-amine / 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 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

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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)42,6656
Polymers42,3102
Non-polymers3554
Water5,296294
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3493
Polymers21,1551
Non-polymers1942
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)21,3163
Polymers21,1551
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.777, 64.725, 75.052
Angle α, β, γ (deg.)90.000, 126.208, 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 2 or resid 4...
d_2ens_1(chain "B" and (resid 1 through 2 or resid 4...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAGLNA1 - 2
d_12ens_1GLULEUA4 - 23
d_13ens_1PHEPHEA25 - 36
d_14ens_1VALSERA39 - 43
d_15ens_1ASNGLYA45 - 66
d_16ens_1LEUALAA68 - 105
d_17ens_1ASPILEA107 - 113
d_18ens_1ALAGLYA115 - 119
d_19ens_1GLULYSA121 - 132
d_110ens_1LEUALAA134 - 136
d_111ens_1GLNLEUA138 - 161
d_112ens_1PROLEUA163 - 185
d_113ens_1GLULYSA187 - 188
d_114ens_1H8H8C
d_21ens_1ALAGLND1 - 2
d_22ens_1GLULEUD4 - 23
d_23ens_1PHEPHED25 - 36
d_24ens_1VALSERD39 - 43
d_25ens_1ASNGLYD45 - 66
d_26ens_1LEUALAD68 - 105
d_27ens_1ASPILED107 - 113
d_28ens_1ALAGLYD115 - 119
d_29ens_1GLULYSD121 - 132
d_210ens_1LEUALAD134 - 136
d_211ens_1GLNLEUD138 - 161
d_212ens_1PROLEUD163 - 185
d_213ens_1GLULYSD187 - 188
d_214ens_1H8H8F

NCS oper: (Code: givenMatrix: (-0.953353081533, 0.0868354065418, 0.289097758728), (-0.29562453714, -0.0749695186335, -0.952357970679), (-0.0610248717474, -0.993397797182, 0.0971430984766)Vector: 32. ...NCS oper: (Code: given
Matrix: (-0.953353081533, 0.0868354065418, 0.289097758728), (-0.29562453714, -0.0749695186335, -0.952357970679), (-0.0610248717474, -0.993397797182, 0.0971430984766)
Vector: 32.8729161671, 14.7628389713, 19.9186725839)

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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-Q3F / 1-methyl-1H-pyrazol-4-amine


Mass: 97.118 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7N3 / 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.: 294 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
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→48.96 Å / Num. obs: 73888 / % possible obs: 97.5 % / Redundancy: 7 % / Biso Wilson estimate: 19.67 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.031 / Rrim(I) all: 0.058 / Χ2: 0.53 / Net I/σ(I): 12.9
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3239 / CC1/2: 0.749 / Rpim(I) all: 0.488 / Rrim(I) all: 0.933 / Χ2: 0.38 / % possible all: 87.4

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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: 1.6→32.36 Å / SU ML: 0.1072 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.9353
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2004 752 1.3 %
Rwork0.1842 57240 -
obs0.1844 57992 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2885 0 22 294 3201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793095
X-RAY DIFFRACTIONf_angle_d0.94484225
X-RAY DIFFRACTIONf_chiral_restr0.0551458
X-RAY DIFFRACTIONf_plane_restr0.0067582
X-RAY DIFFRACTIONf_dihedral_angle_d4.5023437
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.10313778373 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.720.21521580.188211219X-RAY DIFFRACTION97.04
1.72-1.90.23071380.191911377X-RAY DIFFRACTION97.67
1.9-2.170.21281430.193111399X-RAY DIFFRACTION98.14
2.17-2.740.2351530.196511501X-RAY DIFFRACTION98.69
2.74-32.360.17591600.173811744X-RAY DIFFRACTION99.27
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)
10.4577991112530.5446360087020.8442576141342.535072239671.628970613891.377289839390.005823659567510.140262125153-0.115325402768-0.2151421638770.104488591244-0.0990938536424-0.003283290773120.0489483460029-0.06781060764380.202341955519-0.03321730839710.02346118427790.191348625529-0.02660797745960.18417068902230.4373913867-2.744050444341.27463480185
21.220816106010.6700323544990.5633972128751.326194065490.572195458090.896940255046-0.03035653404390.0971780545164-0.0772281583112-0.0620346136830.0506539974173-0.0584623613664-0.004266331290690.0612375366324-0.02297939053670.119697478249-0.007791598294310.01078162889770.1227852635740.008934073535220.12707146093132.83527912911.475625525789.27499366792
31.07146539772-0.02286162896350.1325261575121.3591243080.205388245071.4989076167-0.0513344358303-0.1124564260860.142148014437-0.0272505305722-0.003975495727220.124532126511-0.267997903505-0.1898497681450.04455785803860.2109536483370.0150313766171-0.01962719334420.179232075278-0.02486334515570.189363065835.157391301847.3068239933520.0214205786
43.49120553939-1.21178683102-0.6662330143961.427417915710.5276475577591.42134660593-0.173235140993-0.149838001362-0.2597998393860.301836308170.08332795863490.256473246780.229625179126-0.1766919988930.1078005708420.217406369914-0.01349863711040.03853064716570.208502133383-0.01177040114780.2284353365045.566704451921.7271856873830.3643173706
51.750790778340.2726337785360.6863603665841.842330821810.3362694344831.050292213120.0556307586262-0.08317224455580.1070524049890.0169374987118-0.07669718555180.1439567751220.0733670118323-0.06498171934740.02354626803740.168646752565-0.0175085645635-0.003520104529950.174959962838-0.01800379996280.1606555926594.18969624959-6.7937909119816.409431065
61.93484459140.597267632568-1.003482907670.98818297405-0.7699285866690.869379088852-0.125121688040.0646830002612-0.4339261564330.04092704685770.00501538106932-0.291395860809-0.00960132692376-0.05304930375690.07556002481670.1684609128310.01171790393970.01322143300080.166401774216-0.005041960598910.22504312548311.6169623135-18.143046124814.2245530344
71.78401302585-0.1902706047941.315879168440.9254858549340.1737471090481.872486857280.0259151830284-0.0381860493201-0.314528246032-0.1142767570170.07727387422530.0375173082170.12116263469-0.16493907597-0.08825427274810.152657111121-0.02840953564990.008190733310480.2036812926870.0005396324678910.202632793492-1.3771572462-20.958321827712.655724038
81.173576069051.12095961030.02756170104013.15057806345-0.2190718989090.574517771614-0.1515441784050.02645279496120.210786992038-0.3222826610510.1203267298860.523895608395-0.13444269923-0.2264859492030.07352490820190.2256149862480.00813769003856-0.07981843622220.2326234949930.00575310784790.237857073635-4.75368649234-3.481311568458.0287350559
92.44803559096-1.06225945847-0.4410471845452.749679195731.03765708992.60501398972-0.00441937948013-0.05653544513040.173805665757-0.354163483267-0.06212909847650.391589354717-0.594862613572-0.3753781561610.04884727283180.2495762798510.0291058077892-0.04444656658610.2280726404850.01014708170320.2451409439862.159814042349.7986581882615.595849156
101.70002501777-0.0440673845720.4506352477661.75595081086-0.1801223794822.75791812668-0.12371824783-0.1704592712820.2554505647130.05428811175140.002894601996520.0432045729628-0.419261758189-0.06757581668660.106234029930.2251704724450.01016328311640.01024646650240.185960024703-0.04952475870670.1911474929937.0893325388612.067985333428.4862401629
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 188 )AA66 - 18866 - 188
33chain 'B' and (resid 1 through 38 )BD1 - 381 - 38
44chain 'B' and (resid 39 through 49 )BD39 - 4939 - 49
55chain 'B' and (resid 50 through 97 )BD50 - 9750 - 97
66chain 'B' and (resid 98 through 114 )BD98 - 11498 - 114
77chain 'B' and (resid 115 through 128 )BD115 - 128115 - 128
88chain 'B' and (resid 129 through 144 )BD129 - 144129 - 144
99chain 'B' and (resid 145 through 161 )BD145 - 161145 - 161
1010chain 'B' and (resid 162 through 188 )BD162 - 188162 - 188

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