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- PDB-6sdx: Salmonella ATPase InvC with ATP gamma S -

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Basic information

Entry
Database: PDB / ID: 6sdx
TitleSalmonella ATPase InvC with ATP gamma S
ComponentsATP synthase
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 ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / 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 ...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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / protein-secreting ATPase / SPI-1 type 3 secretion system ATPase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.645 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
DepositionJul 29, 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

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Assembly

Deposited unit
A: ATP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0198
Polymers40,0791
Non-polymers9407
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-26 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.898, 107.898, 73.847
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein ATP synthase / ATP synthase SpeL / FliI/YscN family ATPase


Mass: 40078.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: invC, C2253_13110, CET98_05410, D7F20_20040, D7H43_13080, DD95_05410, DJ388_12235, EKL42_12020
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0D6IHD2, UniProt: P0A1B9*PLUS
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.25 Å3/Da / Density % sol: 62.14 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: 3M sodium chloride pH 7.5 and 0.1 M Tris

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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: Jul 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.645→100 Å / Num. obs: 14402 / % possible obs: 99.8 % / Redundancy: 10 % / CC1/2: 1 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.106 / Net I/σ(I): 16.58
Reflection shellResolution: 2.645→2.71 Å / Rmerge(I) obs: 1.596 / Num. unique obs: 1041 / CC1/2: 0.54 / Rrim(I) all: 1.694

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SWJ

5swj


Resolution: 2.645→53.949 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.51
RfactorNum. reflection% reflection
Rfree0.2236 708 4.92 %
Rwork0.1862 --
obs0.1881 14382 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 184.98 Å2 / Biso mean: 79.3196 Å2 / Biso min: 39.19 Å2
Refinement stepCycle: final / Resolution: 2.645→53.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 57 33 2767
Biso mean--105.98 71.17 -
Num. residues----347
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.645-2.8490.36341430.3105269899
2.849-3.13570.25391420.22932703100
3.1357-3.58940.23691400.19642734100
3.5894-4.52190.21411410.16132748100
4.5219-53.9490.19651420.17122791100
Refinement TLS params.Method: refined / Origin x: 43.3427 Å / Origin y: -6.9601 Å / Origin z: 5.6188 Å
111213212223313233
T0.619 Å2-0.0269 Å2-0.027 Å2-0.3846 Å20.0187 Å2--0.4717 Å2
L0.8506 °20.3259 °20.399 °2-1.264 °20.4375 °2--0.994 °2
S-0.1258 Å °0.0358 Å °0.0813 Å °-0.0894 Å °0.0314 Å °0.155 Å °-0.1664 Å °-0.1433 Å °-0.0032 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA82 - 438
2X-RAY DIFFRACTION1allL1 - 7
3X-RAY DIFFRACTION1allS1 - 33

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