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- PDB-7z3c: A novel molecular switch controls assembly of bacterial focal adh... -

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Basic information

Entry
Database: PDB / ID: 7z3c
TitleA novel molecular switch controls assembly of bacterial focal adhesions in response to changes in surface structure.
ComponentsAdventurous gliding motility protein GltJ
KeywordsCELL ADHESION / protein / motility / GYF domain / myxococcus xanthus / adventurous motility / gliding / focal adhesion complex / adhesion / regulatory domain / myxobacteria
Function / homologyZinc finger/thioredoxin putative / zinc-ribbon domain / GYF domain 2 / GYF domain 2 / Adventurous gliding motility protein GltJ
Function and homology information
Biological speciesMyxococcus xanthus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAttia, B. / My, L. / Castaing, J.P. / Le Guenno, H. / Espinosa, L. / Schmidt, V. / Nouailler, M. / Bornet, O. / Elantak, L. / Mignot, T.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: To Be Published
Title: A novel molecular switch controls assembly of bacterial focal adhesions
Authors: Attia, B. / My, L. / Castaing, J.P. / Dinet, C. / Le Guenno, H. / Schmidt, V. / Espinosa, L. / Anantharaman, V. / Aravind, L. / Sebban-Kreuzer, C. / Nouailler, M. / Bornet, O. / Viollier, P. ...Authors: Attia, B. / My, L. / Castaing, J.P. / Dinet, C. / Le Guenno, H. / Schmidt, V. / Espinosa, L. / Anantharaman, V. / Aravind, L. / Sebban-Kreuzer, C. / Nouailler, M. / Bornet, O. / Viollier, P. / Elantak, L. / Mignot, T.
History
DepositionMar 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adventurous gliding motility protein GltJ


Theoretical massNumber of molelcules
Total (without water)9,3291
Polymers9,3291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 100target function
RepresentativeModel #1medoid

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Components

#1: Protein Adventurous gliding motility protein GltJ


Mass: 9329.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: gltJ, HNV27_16755 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7Y4JDV0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY
131isotropic13D 1H-13C NOESY aliphatic
141isotropic13D 1H-13C NOESY aromatic
151isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] GYF, 90% H2O/10% D2O
Label: 15N_13C / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: GYF / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.1 mM / Label: c1 / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 303 K / Temperature err: 1

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: IMM

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 19

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