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- PDB-4oyc: Crystal structure of the PrgK periplasmic domain 2 -

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Basic information

Entry
Database: PDB / ID: 4oyc
TitleCrystal structure of the PrgK periplasmic domain 2
ComponentsLipoprotein PrgK
KeywordsPROTEIN TRANSPORT / T3SS / macromolecular assembly / inner-membrane
Function / homology
Function and homology information


protein secretion / cell outer membrane
Similarity search - Function
Type III secretion system lipoprotein HrcJ/YscJ / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / ANL, C-terminal domain / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBergeron, J.R.C. / Strynadka, N.C.J.
CitationJournal: Structure / Year: 2015
Title: The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body.
Authors: Julien R C Bergeron / Liam J Worrall / Soumya De / Nikolaos G Sgourakis / Adrienne H Cheung / Emilie Lameignere / Mark Okon / Gregory A Wasney / David Baker / Lawrence P McIntosh / Natalie C J Strynadka /
Abstract: The type III secretion system (T3SS) is a large macromolecular assembly found at the surface of many pathogenic Gram-negative bacteria. Its role is to inject toxic "effector" proteins into the cells ...The type III secretion system (T3SS) is a large macromolecular assembly found at the surface of many pathogenic Gram-negative bacteria. Its role is to inject toxic "effector" proteins into the cells of infected organisms. The molecular details of the assembly of this large, multimembrane-spanning complex remain poorly understood. Here, we report structural, biochemical, and functional analyses of PrgK, an inner-membrane component of the prototypical Salmonella typhimurium T3SS. We have obtained the atomic structures of the two ring building globular domains and show that the C-terminal transmembrane helix is not essential for assembly and secretion. We also demonstrate that structural rearrangement of the two PrgK globular domains, driven by an interconnecting linker region, may promote oligomerization into ring structures. Finally, we used electron microscopy-guided symmetry modeling to propose a structural model for the intimately associated PrgH-PrgK ring interaction within the assembled basal body.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoprotein PrgK
B: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)24,0152
Polymers24,0152
Non-polymers00
Water1267
1
A: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)12,0071
Polymers12,0071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipoprotein PrgK


Theoretical massNumber of molelcules
Total (without water)12,0071
Polymers12,0071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.190, 34.740, 64.030
Angle α, β, γ (deg.)90.00, 110.77, 90.00
Int Tables number5
Space group name H-MC121
DetailsOligomeric state is 24-mer as determined by Electron Microscopy

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Components

#1: Protein Lipoprotein PrgK


Mass: 12007.386 Da / Num. of mol.: 2 / Fragment: 96-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: prgK, STM2871 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41786
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.67 Å3/Da / Density % sol: 26.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate pH 5.5, 20 % PEG 6000, 50 mM NaCl, 50 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→36.09 Å / Num. obs: 4992 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 54.04 Å2 / Net I/σ(I): 4.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YJ7

1yj7


Resolution: 2.6→36.09 Å / Cor.coef. Fo:Fc: 0.8703 / Cor.coef. Fo:Fc free: 0.8491 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.341
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 276 5.53 %RANDOM
Rwork0.2273 ---
obs0.229 4992 98.95 %-
Displacement parametersBiso mean: 48.68 Å2
Baniso -1Baniso -2Baniso -3
1-14.7306 Å20 Å2-0.3369 Å2
2---33.1022 Å20 Å2
3---18.3717 Å2
Refine analyzeLuzzati coordinate error obs: 0.381 Å
Refinement stepCycle: LAST / Resolution: 2.6→36.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 0 7 1344
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091357HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.091832HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d475SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes32HARMONIC2
X-RAY DIFFRACTIONt_gen_planes197HARMONIC5
X-RAY DIFFRACTIONt_it1357HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.2
X-RAY DIFFRACTIONt_other_torsion20.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion181SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1455SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.91 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3191 72 5.26 %
Rwork0.2513 1296 -
all0.2551 1368 -
obs--98.95 %

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