[English] 日本語
Yorodumi
- PDB-6rad: Salmonella ATPase InvC with ADP -

+
Open data


ID or keywords:

Loading...

-
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-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / 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-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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 5 types, 23 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-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


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


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


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


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more