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- PDB-6xfk: Crystal structure of the type III secretion system pilotin-secret... -

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Basic information

Entry
Database: PDB / ID: 6xfk
TitleCrystal structure of the type III secretion system pilotin-secretin complex InvH-InvG
Components
  • Type 3 secretion system pilotinType three secretion system
  • Type 3 secretion system secretinType three secretion system
KeywordsPROTEIN TRANSPORT / pilotin / secretin / chaperone / type III secretion
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
InvH outer membrane lipoprotein / InvH outer membrane lipoprotein / : / 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 ...InvH outer membrane lipoprotein / InvH outer membrane lipoprotein / : / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
SPI-1 type 3 secretion system pilotin / SPI-1 type 3 secretion system secretin
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMajewski, D.D. / Okon, M. / Heinkel, F. / Robb, C.S. / Vuckovic, M. / McIntosh, L.P. / Strynadka, N.C.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Structure / Year: 2021
Title: Characterization of the Pilotin-Secretin Complex from the Salmonella enterica Type III Secretion System Using Hybrid Structural Methods.
Authors: Majewski, D.D. / Okon, M. / Heinkel, F. / Robb, C.S. / Vuckovic, M. / McIntosh, L.P. / Strynadka, N.C.J.
History
DepositionJun 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: Type 3 secretion system pilotin
B: Type 3 secretion system secretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3064
Polymers10,1142
Non-polymers1922
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-39 kcal/mol
Surface area4870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.313, 36.313, 221.602
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-359-

HOH

21B-605-

HOH

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Components

#1: Protein Type 3 secretion system pilotin / Type three secretion system / Invasion lipoprotein invH


Mass: 8090.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: invH, sctG, STM2900 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CL43
#2: Protein/peptide Type 3 secretion system secretin / Type three secretion system / T3SS secretin / Protein InvG


Mass: 2023.296 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P35672
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.5 M lithium sulfate, 8.3% PEG 6000, 100 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→36.93 Å / Num. obs: 8226 / % possible obs: 99.5 % / Redundancy: 16.5 % / CC1/2: 1 / Net I/σ(I): 16.8
Reflection shellResolution: 1.85→1.92 Å / Num. unique obs: 788 / CC1/2: 0.908

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XFJ

6xfj


Resolution: 1.85→36.93 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.794 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 420 5.1 %RANDOM
Rwork0.2175 ---
obs0.2189 7768 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.6 Å2 / Biso mean: 43.558 Å2 / Biso min: 27.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0.25 Å20 Å2
2---0.5 Å20 Å2
3---1.63 Å2
Refinement stepCycle: final / Resolution: 1.85→36.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms618 0 10 69 697
Biso mean--59.76 64.57 -
Num. residues----74
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.013650
X-RAY DIFFRACTIONr_bond_other_d0.0010.017587
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.658876
X-RAY DIFFRACTIONr_angle_other_deg1.4491.5831360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.247574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.53822.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79315120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.869155
X-RAY DIFFRACTIONr_chiral_restr0.0950.279
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02708
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02143
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 27 -
Rwork0.254 544 -
all-571 -
obs--99.65 %
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)
15.75972.05650.82922.24431.21933.86150.0493-0.2619-0.1060.0709-0.1899-0.08740.2668-0.0510.14070.1230.01570.00260.1429-0.09470.10452.02513.2446.359
23.61542.3308-1.33346.82681.89458.56150.1954-0.41670.18390.5958-0.3940.47540.3848-0.44350.19870.1215-0.02730.00550.1666-0.08840.08040.65315.06913.957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A84 - 146
2X-RAY DIFFRACTION2B546 - 556

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