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- PDB-4g08: Crystal structure of the periplasmic domain of InvG -

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Basic information

Entry
Database: PDB / ID: 4g08
TitleCrystal structure of the periplasmic domain of InvG
ComponentsProtein InvG
KeywordsCELL INVASION / Ring-building motif / protein secretion / PrgH
Function / homology
Function and homology information


type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / protein secretion / cell outer membrane / identical protein binding
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #120 / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain ...Ribosomal Protein S8; Chain: A, domain 1 - #120 / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / : / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein / 3-Layer(bab) Sandwich / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SPI-1 type 3 secretion system secretin
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.801 Å
AuthorsBergeron, J.R.C. / Strynadka, N.C.J.
CitationJournal: PLoS Pathog / Year: 2013
Title: A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly.
Authors: Julien R C Bergeron / Liam J Worrall / Nikolaos G Sgourakis / Frank DiMaio / Richard A Pfuetzner / Heather B Felise / Marija Vuckovic / Angel C Yu / Samuel I Miller / David Baker / Natalie C J Strynadka /
Abstract: The T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence effectors into host cells. It is composed ...The T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence effectors into host cells. It is composed of a "basal body", a lock-nut structure spanning both bacterial membranes, and a "needle" that protrudes away from the bacterial surface. A hollow channel spans throughout the apparatus, permitting the translocation of effector proteins from the bacterial cytosol to the host plasma membrane. The basal body is composed largely of three membrane-embedded proteins that form oligomerized concentric rings. Here, we report the crystal structures of three domains of the prototypical Salmonella SPI-1 basal body, and use a new approach incorporating symmetric flexible backbone docking and EM data to produce a model for their oligomeric assembly. The obtained models, validated by biochemical and in vivo assays, reveal the molecular details of the interactions driving basal body assembly, and notably demonstrate a conserved oligomerization mechanism.
History
DepositionJul 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein InvG


Theoretical massNumber of molelcules
Total (without water)17,8381
Polymers17,8381
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.270, 56.660, 74.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThough the cloned protein construct that was crystallized is a monomer, the full-length version of this protein forms a 15-mer.

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Components

#1: Protein Protein InvG


Mass: 17838.301 Da / Num. of mol.: 1 / Fragment: UNP residues 22-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: invG, STM2898 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35672
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 1.67 Å3/Da / Density % sol: 26.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris, pH 8.0, 30% Jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.978170, 0.979310, 0.979100
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 7, 2010
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978171
20.979311
30.97911
ReflectionResolution: 1.8→50 Å / Num. all: 11629 / Num. obs: 11517 / % possible obs: 99.3 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 18.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 7.3 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
SOLVEphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MxDCdata collection
RefinementMethod to determine structure: MAD / Resolution: 1.801→45.086 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU ML: 0.2 / σ(F): 1.36 / Phase error: 23.37 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.2308 547 4.75 %
Rwork0.1903 --
obs0.192 11516 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.562 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2--0.64 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.801→45.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 0 0 112 1229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011175
X-RAY DIFFRACTIONf_angle_d1.0511590
X-RAY DIFFRACTIONf_dihedral_angle_d15.763450
X-RAY DIFFRACTIONf_chiral_restr0.067170
X-RAY DIFFRACTIONf_plane_restr0.021208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.801-1.98250.26731470.21242630X-RAY DIFFRACTION98
1.9825-2.26930.23871320.19752709X-RAY DIFFRACTION99
2.2693-2.8590.24491390.20692754X-RAY DIFFRACTION100
2.859-45.09970.21141290.17722876X-RAY DIFFRACTION99

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