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- PDB-7pqf: Crystal structure of Campylobacter jejuni DsbA2 -

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Basic information

Entry
Database: PDB / ID: 7pqf
TitleCrystal structure of Campylobacter jejuni DsbA2
ComponentsThiol:disulfide interchange protein DsbA/DsbL
KeywordsOXIDOREDUCTASE / periplasmic / disulfide bond / thioredoxin fold / posttranslational modification
Function / homologyThiol:disulphide interchange protein DsbA/DsbL / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / periplasmic space / Thiol:disulfide interchange protein DsbA/DsbL
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWilk, P. / Banas, A.M. / Bocian-Ostrzycka, K.M. / Jagusztyn-Krynicka, E.K.
Funding support Poland, 2items
OrganizationGrant numberCountry
Foundation for Polish ScienceFACILITY/2017-4/6 Poland
Polish National Science Centre2015/17/B/NZ1/00230 Poland
CitationJournal: Int J Mol Sci / Year: 2021
Title: Interplay between DsbA1, DsbA2 and C8J_1298 Periplasmic Oxidoreductases of Campylobacter jejuni and Their Impact on Bacterial Physiology and Pathogenesis.
Authors: Banas, A.M. / Bocian-Ostrzycka, K.M. / Dunin-Horkawicz, S. / Ludwiczak, J. / Wilk, P. / Orlikowska, M. / Wyszynska, A. / Dabrowska, M. / Plichta, M. / Spodzieja, M. / Polanska, M.A. / ...Authors: Banas, A.M. / Bocian-Ostrzycka, K.M. / Dunin-Horkawicz, S. / Ludwiczak, J. / Wilk, P. / Orlikowska, M. / Wyszynska, A. / Dabrowska, M. / Plichta, M. / Spodzieja, M. / Polanska, M.A. / Malinowska, A. / Jagusztyn-Krynicka, E.K.
History
DepositionSep 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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/DsbL


Theoretical massNumber of molelcules
Total (without water)23,3861
Polymers23,3861
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.491, 43.491, 196.312
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Thiol:disulfide interchange protein DsbA/DsbL


Mass: 23385.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter)
Gene: BCB47_05860, DPG08_09260, EC071_03680, F8Y55_09670, F9778_05070, FVY60_01405, FW488_04095, FZ445_05600, FZ732_06725, GNO00_06025, GXA88_04900, GXS76_000976
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: A0A1J6UFJ6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: LMB F5 condition (29% w/v PEG 4000, 0.1M Sodium citrate, 0.1M Magnesium acetate tetrahydrate, 0.1M Ammonium sulfate, pH 6.5). Starting protein concentration 130 mg/ml.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 18, 2021
RadiationMonochromator: double-channel cut fixed-exit monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→39.26 Å / Num. obs: 20471 / % possible obs: 99.2 % / Redundancy: 13.86 % / Biso Wilson estimate: 33.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.121 / Net I/σ(I): 14.6
Reflection shellResolution: 1.81→1.92 Å / Redundancy: 13.89 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 3072 / CC1/2: 0.632 / Rrim(I) all: 0.2817 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PQ7

7pq7


Resolution: 1.82→37.66 Å / SU ML: 0.2754 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.0378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2347 1017 5 %
Rwork0.199 19333 -
obs0.2008 20350 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.93 Å2
Refinement stepCycle: LAST / Resolution: 1.82→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 0 0 107 1661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941616
X-RAY DIFFRACTIONf_angle_d1.01282186
X-RAY DIFFRACTIONf_chiral_restr0.0559231
X-RAY DIFFRACTIONf_plane_restr0.0066283
X-RAY DIFFRACTIONf_dihedral_angle_d5.34061373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.910.41111350.39732588X-RAY DIFFRACTION96.02
1.91-2.030.31381430.28122710X-RAY DIFFRACTION99.69
2.03-2.190.28531440.23832741X-RAY DIFFRACTION99.97
2.19-2.410.28261440.21882728X-RAY DIFFRACTION99.62
2.41-2.760.25861450.20152760X-RAY DIFFRACTION99.93
2.76-3.470.27241480.20612811X-RAY DIFFRACTION99.97
3.47-37.660.17361580.1632995X-RAY DIFFRACTION100
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)
10.229398695827-0.1380018615550.07967872123270.677486879179-0.3012879010860.1222689804330.356880218269-0.06112663666840.3805196111810.3102034781420.1537155465710.135671320121-0.712200346746-0.4586595654020.008102390484380.5214398778140.09531391672140.1861545111260.5083616217050.1055985265050.46482698807811.60991417498.41515720456-21.0369354169
20.283064836744-0.368271751973-0.2584202830580.6257197582860.005404421113990.4112209678810.07055435537920.09695095371560.0318784911643-0.3412687170110.0295804355195-0.221261022454-0.002268408589960.082241373002-0.0001976267689820.436232233599-0.0331207741260.06242817193220.331507311177-0.004146048136930.38204130477322.2560482584-6.76204889652-22.5686459749
30.275208010914-0.213225126129-0.667174000420.6065275807270.2821881905321.56482457342-0.0579584268852-0.1832353808090.01212029187280.03267249798340.0251524438769-0.00502138605998-0.1927172167130.1598617940540.001544259908640.341775251643-0.06140573100310.04205012111960.2868870227520.009462916494670.33692202011320.6822847498-6.67674340663-10.735442765
40.06465984387240.274500002931-0.2286618844010.959379526131-0.7062429528240.64608434078-0.4763493887680.037778058313-0.0989227317821-1.097762754110.0887913508397-0.4086718192090.1974776588780.418818438338-0.02663275418510.371617405271-0.000952061885890.1050999580620.364292251456-0.01051911966340.41820856468427.7776393131-11.5220843913-15.5614642923
51.858945173280.278227098229-1.841179981871.061386793740.1148795062422.07052873803-0.631532953144-0.134479896233-0.398362336008-0.3161357775520.0713015974539-0.06473749675871.162665144720.307821995488-0.60612866120.632905361166-0.004202046139150.1272313234220.230910803639-3.50283705697E-50.45316049792419.5918179243-23.2549338401-10.3184282769
60.513885111590.614526287905-0.1127950878092.686020963310.1088460733090.0578155440235-0.302807695398-0.4501989455490.3140839874411.470009899020.168419558091-0.05638653513510.7214176711020.550035508048-0.007053074567040.458680017330.0677347167496-0.01763484379480.4119969809230.01859664747110.32348071472824.5395769561-13.24306740752.07762893311
70.0157578578755-0.1200104590410.03650017360560.449129972945-0.1664726320370.0501131567833-0.0607218315812-0.2217439496150.3064328479340.1533763683450.01700209927740.200835235955-0.50622936147-0.53641219698-0.001133888608330.3815721117870.01125799483630.0331084848290.38256016627-0.001220847155690.36935749947212.2784670105-2.79040093718-9.92492478423
80.574012041839-0.00976245864992-0.141375169670.296789192266-0.1920968743880.1569744416690.2758124974220.395176816794-0.0894628214196-0.269806182897-0.131324514702-0.164931124389-0.400893670963-0.4060468598950.01901756704550.5914174804380.03623124325940.09370443022550.3570430618340.0382634589950.35534825419614.58736837871.77623885126-24.8248204529
90.372014535893-0.1702090261070.2175787075280.159008302846-0.04728082421590.1494666545650.4932364927130.7396049881190.647794618627-0.518255675919-0.413172458404-0.377088824062-0.38380403222-0.06151076043850.01094813426530.59513013520.06849201492330.1207377720480.3324706601370.09786995529020.42435158968121.79484841917.62895878681-28.2704436442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 81 )
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 105 )
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 128 )
6X-RAY DIFFRACTION6chain 'A' and (resid 129 through 141 )
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 161 )
8X-RAY DIFFRACTION8chain 'A' and (resid 162 through 181 )
9X-RAY DIFFRACTION9chain 'A' and (resid 182 through 194 )

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