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- PDB-6rae: Structural analysis of the Salmonella type III secretion system A... -

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Basic information

Entry
Database: PDB / ID: 6rae
TitleStructural analysis of the Salmonella type III secretion system ATPase InvC
ComponentsSecretory apparatus ATP synthase (Associated with virulence)
KeywordsHYDROLASE / Bacterial pathogenesis / Salmonella enterica / Type III secretion system (T3SS) / ATPase / Crystallography.
Function / homology
Function and homology information


protein-exporting ATPase activity / protein-secreting ATPase / type III protein secretion system complex / protein secretion by the type III secretion system / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / proton transmembrane transport / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP hydrolysis activity ...protein-exporting ATPase activity / protein-secreting ATPase / type III protein secretion system complex / protein secretion by the type III secretion system / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / proton transmembrane transport / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities ...ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
protein-secreting ATPase / SPI-1 type 3 secretion system ATPase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.049 Å
AuthorsBernal, I. / Roemermann, J. / Flacht, L. / Lunelli, M. / Uetrecht, C. / Kolbe, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme311374 Germany
CitationJournal: Protein Sci. / Year: 2019
Title: Structural analysis of ligand-bound states of the Salmonella type III secretion system ATPase InvC.
Authors: Bernal, I. / Romermann, J. / Flacht, L. / Lunelli, M. / Uetrecht, C. / Kolbe, M.
History
DepositionApr 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Secretory apparatus ATP synthase (Associated with virulence)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2424
Polymers40,0791
Non-polymers1633
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-25 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.292, 106.292, 73.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Secretory apparatus ATP synthase (Associated with virulence)


Mass: 40078.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain SL1344) (bacteria)
Strain: SL1344 / Gene: invC, SL1344_2873 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3NGZ8, UniProt: P0A1B9*PLUS
#2: 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
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.99 Å3/Da / Density % sol: 58.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.8 M succinic acid pH 7.0 and 30 % (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.049→92.05 Å / Num. obs: 29753 / % possible obs: 99.92 % / Redundancy: 7.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.109 / Net I/σ(I): 11.35
Reflection shellResolution: 2.049→2.122 Å / Rmerge(I) obs: 1.091 / Num. unique obs: 2925 / CC1/2: 0.66 / Rrim(I) all: 1.167

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SWJ

5swj


Resolution: 2.049→92.05 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.29
RfactorNum. reflection% reflection
Rfree0.2065 1487 5 %
Rwork0.1643 --
obs0.1664 29752 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.049→92.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2711 0 8 151 2870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062764
X-RAY DIFFRACTIONf_angle_d0.7973741
X-RAY DIFFRACTIONf_dihedral_angle_d20.0191682
X-RAY DIFFRACTIONf_chiral_restr0.049424
X-RAY DIFFRACTIONf_plane_restr0.005491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0491-2.11520.28251340.23712535X-RAY DIFFRACTION99
2.1152-2.19080.24351340.2172553X-RAY DIFFRACTION100
2.1908-2.27850.23141340.1982549X-RAY DIFFRACTION100
2.2785-2.38220.22611340.19492560X-RAY DIFFRACTION100
2.3822-2.50780.22321340.19112559X-RAY DIFFRACTION100
2.5078-2.66490.20911360.19842574X-RAY DIFFRACTION100
2.6649-2.87070.21631360.19092582X-RAY DIFFRACTION100
2.8707-3.15950.23331340.192561X-RAY DIFFRACTION100
3.1595-3.61660.19691360.17022566X-RAY DIFFRACTION100
3.6166-4.55620.19971360.13452591X-RAY DIFFRACTION100
4.5562-53.16390.18441390.13942635X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 41.7299 Å / Origin y: -7.1983 Å / Origin z: 4.8446 Å
111213212223313233
T0.3753 Å20.01 Å20.0521 Å2-0.2936 Å20.0204 Å2--0.3227 Å2
L1.1155 °20.4776 °20.9699 °2-1.2419 °20.5232 °2--1.8259 °2
S-0.0443 Å °-0.0411 Å °-0.038 Å °-0.0938 Å °0.06 Å °0.0622 Å °-0.2804 Å °-0.1955 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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