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- PDB-1y6d: Solution structure and dynamics of LuxU from Vibrio harveyi, a ph... -

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Basic information

Entry
Database: PDB / ID: 1y6d
TitleSolution structure and dynamics of LuxU from Vibrio harveyi, a phosphotransferase protein involved in bacterial quorum sensing
ComponentsPhosphorelay protein luxU
KeywordsTRANSFERASE / phosphotransferase / four-helix bundle / quorum sensing / phosphorelay
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
HPT domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphorelay protein LuxU / Phosphorelay protein LuxU
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodSOLUTION NMR
AuthorsUlrich, D.L. / Kojetin, D. / Bassler, B.L. / Cavanagh, J. / Loria, J.P.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Solution structure and dynamics of LuxU from Vibrio harveyi, a phosphotransferase protein involved in bacterial quorum sensing.
Authors: Ulrich, D.L. / Kojetin, D. / Bassler, B.L. / Cavanagh, J. / Loria, J.P.
#1: Journal: J.BIOMOL.NMR / Year: 2004
Title: 1H,15N,and 13C chemical shift assignments of the Vibrio harveyi histidine phosphotransferase protein LuxU
Authors: Ulrich, D.L. / Thompson, R. / Bassler, B. / Cavanagh, J. / Loria, J.P.
History
DepositionDec 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphorelay protein luxU


Theoretical massNumber of molelcules
Total (without water)13,5301
Polymers13,5301
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 19structures with the lowest energy
RepresentativeModel #17

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Components

#1: Protein Phosphorelay protein luxU


Mass: 13530.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: LuxU / Plasmid: pDLU / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 pLys-S / References: UniProt: Q9ZBB6, UniProt: P0C5S4*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
131HNHA
1423D 13C-separated NOESY
2523D 13C (H)CCH-TOCSY
262HNCA
272HN(CO)CA
282HN(CA)CB

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM LuxU U-15N, 50mM Phosphate buffer, 300mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
21mM LuxU U-15N,13C, 50mM Phosphate buffer, 300mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1300mM NaCl 6.4 ambient 294 K
2300mM NaCl 6.4 ambient 294 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002
Varian UNITYPLUSVarianUNITYPLUS6003
Varian INOVAVarianINOVA8004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipedelaglio,f. et alprocessing
CNS1brunger, a.t. et alstructure solution
Sparkygoddard,t. et aldata analysis
DYANACYANAguntert,p.structure solution
XPLOR-NIHrefinement
TALOSspera,s. and bax,a.data analysis
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 19 / Conformers submitted total number: 19

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