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- PDB-6rad: Salmonella ATPase InvC with ADP -

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Basic information

Entry
Database: PDB / ID: 6rad
TitleSalmonella ATPase InvC with ADP
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
ADENOSINE-5'-DIPHOSPHATE / protein-secreting ATPase / SPI-1 type 3 secretion system ATPase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.796 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Secretory apparatus ATP synthase (Associated with virulence)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,44211
Polymers40,0791
Non-polymers1,36310
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-14 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.449, 107.449, 73.511
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 23 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 1.6 M magnesium sulfate, 0.1 M MES pH 6.5 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: 2.796→43.4 Å / Num. obs: 11871 / % possible obs: 97.76 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.092 / Net I/σ(I): 13.17
Reflection shellResolution: 2.796→2.896 Å / Rmerge(I) obs: 0.804 / Num. unique obs: 11871 / CC1/2: 0.875 / Rrim(I) all: 0.864

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.796→43.375 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.26
RfactorNum. reflection% reflection
Rfree0.2571 591 5 %
Rwork0.2112 --
obs0.2134 11813 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.796→43.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2623 0 86 13 2722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032747
X-RAY DIFFRACTIONf_angle_d0.6443711
X-RAY DIFFRACTIONf_dihedral_angle_d20.7791662
X-RAY DIFFRACTIONf_chiral_restr0.041417
X-RAY DIFFRACTIONf_plane_restr0.005473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7947-3.07580.38311450.31882765X-RAY DIFFRACTION96
3.0758-3.52070.30981510.2512812X-RAY DIFFRACTION99
3.5207-4.43510.2381510.20012817X-RAY DIFFRACTION99
4.4351-43.38050.22891440.18682828X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 43.6845 Å / Origin y: -6.7207 Å / Origin z: 5.7213 Å
111213212223313233
T0.8816 Å20.0333 Å20.0173 Å2-0.4992 Å20.0279 Å2--0.5823 Å2
L0.8312 °20.2648 °20.5191 °2-1.143 °20.3772 °2--1.6268 °2
S-0.0966 Å °0.0371 Å °0.0218 Å °-0.1108 Å °0.0683 Å °0.0801 Å °-0.6218 Å °-0.3133 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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