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- PDB-6pli: Crystal Structure of EcDsbA in a complex with purified oxadiazole 11 -

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Basic information

Entry
Database: PDB / ID: 6pli
TitleCrystal Structure of EcDsbA in a complex with purified oxadiazole 11
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / OXIDOREDUCTASE-INHIBITOR COMPLEX / REFiLX / 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 / Thioredoxin-like superfamily ...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 / Chem-ONY / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsIlyichova, O.V. / Bentley, M. / Doak, B. / Scanlon, M.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)Project Grant APP1099151 Australia
Australian Research Council (ARC)LIEF LE160100047 Australia
CitationJournal: J.Med.Chem. / Year: 2020
Title: Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiL X ).
Authors: Bentley, M.R. / Ilyichova, O.V. / Wang, G. / Williams, M.L. / Sharma, G. / Alwan, W.S. / Whitehouse, R.L. / Mohanty, B. / Scammells, P.J. / Heras, B. / Martin, J.L. / Totsika, M. / Capuano, ...Authors: Bentley, M.R. / Ilyichova, O.V. / Wang, G. / Williams, M.L. / Sharma, G. / Alwan, W.S. / Whitehouse, R.L. / Mohanty, B. / Scammells, P.J. / Heras, B. / Martin, J.L. / Totsika, M. / Capuano, B. / Doak, B.C. / Scanlon, M.J.
History
DepositionJul 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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

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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)42,7644
Polymers42,3102
Non-polymers4542
Water3,297183
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5452
Polymers21,1551
Non-polymers3901
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)117.745, 64.286, 74.444
Angle α, β, γ (deg.)90.000, 125.907, 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 (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-ONY / 2-[4-(4-cyano-3-methylphenoxy)phenyl]-N-methyl-N-[2-(5-methyl-1,2,4-oxadiazol-3-yl)ethyl]acetamide


Mass: 390.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.67 %
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: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2018
RadiationMonochromator: DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.93→34.69 Å / Num. obs: 33581 / % possible obs: 98.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 37.69 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.046 / Rrim(I) all: 0.086 / Χ2: 0.86 / Net I/σ(I): 11
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.691 / Num. unique obs: 1957 / CC1/2: 0.878 / Rpim(I) all: 0.433 / Rrim(I) all: 0.817 / % possible all: 85.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.93→34.69 Å / SU ML: 0.2592 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6487
RfactorNum. reflection% reflection
Rfree0.2275 1583 4.72 %
Rwork0.1979 --
obs0.1993 33540 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.62 Å2
Refinement stepCycle: LAST / Resolution: 1.93→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 30 183 3087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873000
X-RAY DIFFRACTIONf_angle_d0.73944081
X-RAY DIFFRACTIONf_chiral_restr0.0419448
X-RAY DIFFRACTIONf_plane_restr0.0041535
X-RAY DIFFRACTIONf_dihedral_angle_d6.48682074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.990.37061200.31142615X-RAY DIFFRACTION89.06
1.99-2.060.31041540.27692914X-RAY DIFFRACTION99.71
2.06-2.150.28391340.25212904X-RAY DIFFRACTION99.77
2.15-2.250.31331430.23862937X-RAY DIFFRACTION99.74
2.25-2.360.27181190.23182950X-RAY DIFFRACTION99.93
2.36-2.510.2481480.22422920X-RAY DIFFRACTION99.77
2.51-2.710.26431530.22582925X-RAY DIFFRACTION99.87
2.71-2.980.31181560.22372916X-RAY DIFFRACTION99.9
2.98-3.410.27251460.20992941X-RAY DIFFRACTION99.94
3.41-4.290.17981560.17242932X-RAY DIFFRACTION99.48
4.29-34.70.17661540.16223003X-RAY DIFFRACTION99.46
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)
11.005723119580.7090479724151.079282644074.805859008143.541969276893.664949287950.008050660956460.211056426424-0.0963703490412-0.1916835549110.0365318964298-0.06683810068770.004742614680750.120449729241-0.01503927936090.340312767836-0.0121329894555-0.001051738788010.314160188492-0.02224373255430.29383427116330.9613828952-8.796758608290.849064749242
22.586729572150.8317201846570.3060139177653.078073346690.3716056465454.06448008884-0.121246801488-0.06590762088310.1040799724380.1334894183410.0516470367945-0.1577605234390.2607321023160.3087273642080.07772117331330.2972747668940.0332852847287-0.02079355360380.264814319336-0.005645978350840.25131669453237.2145079679-0.23569129734316.6177278712
31.484388557791.207138326050.6487707437765.074058739941.295335808862.180948727590.08166669776310.1739337361730.103222687397-0.243559130038-0.004722452598830.174057781532-0.1772464444550.0954842041414-0.08380254239520.3407314011240.000325169082613-0.0311939460120.316298597226-0.02891571819220.24035558988226.963140528-13.1027650135-3.47460456124
43.17724219839-0.124976165772-0.3145059703483.09481551465-2.754887921514.428403922910.7033211863880.6591242027180.525932498282-1.13828611226-0.7407413664540.796067308447-1.89937273533-0.7960062107510.1729850895131.232314315290.5195594740010.1743011845240.831132581547-0.07254796261610.8020928050373.040648622111.076689959820.6350278041
54.247391873570.614547855980.7285862124754.663118146192.025928256697.871700271470.2431687799590.3791617588070.314050219055-0.328066376633-0.3210262645740.657723241978-0.166208045497-0.7672391269050.01777597020260.473882184988-0.0009609883145130.0386710492520.346483966875-0.04399097467840.488264403297.07785805247-6.320821558321.5271143681
65.363187574521.18976688089-1.617200414333.594744573210.2790870084962.7090148201-0.0799948508569-0.0988698272548-0.134389798308-0.179844253973-0.1016607519890.264566298923-0.0870154989613-0.122051482560.1650654475180.365066488144-0.00913423107765-0.003679634395640.360469914954-0.02425854093230.3358534454416.46048156291-21.191416684914.2509019178
73.058590151761.385578790061.311507000613.767456236691.058019900422.177685100910.0302246387228-0.05050384604990.701406906122-0.490145958308-0.3258931421670.75318021406-0.7765627986-0.817353160070.2546570639680.824807472850.358832533119-0.002384717793170.7342722462260.008129739462440.5732880863480.851710727401-2.0723969379512.267812306
86.391925769380.8008079170130.3148645446398.76074262362-0.1013769032167.179132289270.707897978015-0.01176728494760.50192102995-0.590573197543-0.8528274389290.0165843526993-0.826965468344-0.3330275700510.1396825790420.7679464782180.1002302192770.1962625922590.382281911754-0.08674803271010.5474862304029.301931887755.3427284104629.127591563
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 21 )
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 65 )
6X-RAY DIFFRACTION6chain 'B' and (resid 66 through 128 )
7X-RAY DIFFRACTION7chain 'B' and (resid 129 through 161 )
8X-RAY DIFFRACTION8chain 'B' and (resid 162 through 188 )

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