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- PDB-7yyg: Crystal structure of gatekeeper of type III secretion system in B... -

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Basic information

Entry
Database: PDB / ID: 7yyg
TitleCrystal structure of gatekeeper of type III secretion system in Bordetella BopN
ComponentsPutative outer protein N
KeywordsIMMUNOSUPPRESSANT / The type III secretion system / Whooping cough / Immunosuppressive modulator / Bordetella pertussis
Function / homology
Function and homology information


protein secretion by the type III secretion system / outer membrane / negative regulation of protein secretion / cell surface
Similarity search - Function
Type III secretion system effector delivery regulator TyeA / TyeA / TyeA superfamily / Type III secretion system effector delivery regulator TyeA-related / Type III secretion regulator, YopN/LcrE/InvE/MxiC / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / Putative outer protein N
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.95 Å
AuthorsPrudnikova, T. / Kuta Smatanova, I. / Kamanova, J. / Bumba, L.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic21-05466S Czech Republic
Czech Academy of SciencesLQ200202001 Czech Republic
Czech Academy of SciencesLM2018133 Czech Republic
CitationJournal: Microbiol Spectr / Year: 2023
Title: BopN is a Gatekeeper of the Bordetella Type III Secretion System.
Authors: Navarrete, K.M. / Bumba, L. / Prudnikova, T. / Malcova, I. / Allsop, T.R. / Sebo, P. / Kamanova, J.
History
DepositionFeb 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 28, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative outer protein N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4377
Polymers39,0371
Non-polymers4006
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.859, 84.859, 102.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-402-

NA

21A-403-

CL

31A-637-

HOH

41A-652-

HOH

51A-660-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative outer protein N


Mass: 39036.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bordetella pertussis Tohama I (bacteria) / Strain: Tohama I / ATCC BAA-589 / NCTC 13251 / References: UniProt: Q79GQ0

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Non-polymers , 7 types, 166 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16M Calcium acetate, 0.08M sodium cacodylate, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.95→43.93 Å / Num. obs: 26601 / % possible obs: 97.5 % / Redundancy: 8.88 % / Biso Wilson estimate: 36.5 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.1 / Net I/σ(I): 18.7
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 1.75 / Num. unique obs: 4088 / CC1/2: 0.73 / Rrim(I) all: 0.127

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.95→43.93 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 7.515 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20709 1400 5 %RANDOM
Rwork0.17968 ---
obs0.18103 26586 99.91 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.007 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 23 160 2250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0172268
X-RAY DIFFRACTIONr_bond_other_d0.0010.022175
X-RAY DIFFRACTIONr_angle_refined_deg0.8581.8783091
X-RAY DIFFRACTIONr_angle_other_deg0.9972.6944991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8255305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.30722.154130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55815372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8521520
X-RAY DIFFRACTIONr_chiral_restr0.0460.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02522
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7792.9251179
X-RAY DIFFRACTIONr_mcbond_other4.772.9191177
X-RAY DIFFRACTIONr_mcangle_it5.4514.3541497
X-RAY DIFFRACTIONr_mcangle_other5.4494.3591498
X-RAY DIFFRACTIONr_scbond_it7.5623.6911089
X-RAY DIFFRACTIONr_scbond_other7.5593.6971090
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.6855.231595
X-RAY DIFFRACTIONr_long_range_B_refined10.36937.6182627
X-RAY DIFFRACTIONr_long_range_B_other10.37637.1572589
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å
RfactorNum. reflection% reflection
Rfree0.325 102 -
Rwork0.3 1933 -
obs--99.85 %
Refinement TLS params.Method: refined / Origin x: 29.004 Å / Origin y: 66.345 Å / Origin z: 5.536 Å
111213212223313233
T0.0775 Å2-0.0333 Å20.0072 Å2-0.0702 Å20.0046 Å2--0.0411 Å2
L0.8919 °20.4761 °20.8115 °2-1.0067 °20.6491 °2--2.1698 °2
S-0.0181 Å °-0.0897 Å °-0.06 Å °0.0013 Å °-0.018 Å °0.1278 Å °0.2461 Å °-0.3253 Å °0.0361 Å °

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