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- PDB-2lfw: NMR structure of the PhyRSL-NepR complex from Sphingomonas sp. Fr1 -

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Basic information

Entry
Database: PDB / ID: 2lfw
TitleNMR structure of the PhyRSL-NepR complex from Sphingomonas sp. Fr1
Components
  • NepR anti sigma factor
  • PhyR sigma-like domain
KeywordsSIGNALING PROTEIN / signal transduction / response regulator / sigma factor mimicry / anti-sigma factor / general stress response
Function / homology
Function and homology information


molecular function inhibitor activity / phosphorelay signal transduction system
Similarity search - Function
Anti-sigma factor NepR / Anti-sigma factor NepR / Signal transduction response regulator PhyR-like, alphaproteobacteria / : / : / Sigma2 domain of PhyR / Response regulator PhyR, sigma-like domain / PhyR, sigma-like (SL) domain / : / Butyryl-CoA Dehydrogenase, subunit A; domain 3 ...Anti-sigma factor NepR / Anti-sigma factor NepR / Signal transduction response regulator PhyR-like, alphaproteobacteria / : / : / Sigma2 domain of PhyR / Response regulator PhyR, sigma-like domain / PhyR, sigma-like (SL) domain / : / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSphingomonas sp. Fr1 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 15
AuthorsCampagne, S. / Damberger, F.F. / Vorholt, J.A. / Allain, F.H.-T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for sigma factor mimicry in the general stress response of Alphaproteobacteria.
Authors: Campagne, S. / Damberger, F.F. / Kaczmarczyk, A. / Francez-Charlot, A. / Allain, F.H. / Vorholt, J.A.
History
DepositionJul 18, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Jun 6, 2012Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5May 15, 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: PhyR sigma-like domain
B: NepR anti sigma factor


Theoretical massNumber of molelcules
Total (without water)24,2592
Polymers24,2592
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 20structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein PhyR sigma-like domain


Mass: 17336.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. Fr1 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: G8HXE0*PLUS
#2: Protein NepR anti sigma factor


Mass: 6923.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. Fr1 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: G8HXD9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR structure of the PhyRSL-NepR complex from Sphingomonas sp. Fr1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1313D HNCO
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D (H)CCH-TOCSY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C HSQC aromatic
1913D 1H-15N NOESY
11023D HNCO
11123D HN(CA)CB
11223D CBCA(CO)NH
11323D (H)CCH-TOCSY
11423D 1H-15N NOESY
11523D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N] PhyR sigma like domain, 0.8 mM NepR anti sigma factor, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM PhyR sigma like domain, 0.8 mM [U-100% 13C; U-100% 15N] NepR anti sigma factor, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMPhyR sigma like domain-1[U-100% 13C; U-100% 15N]1
0.8 mMNepR anti sigma factor-21
0.8 mMPhyR sigma like domain-32
0.8 mMNepR anti sigma factor-4[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.06 / pH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameDeveloperClassification
CARABartels et al.chemical shift assignment
ATNOS_CANDIDGuntert, Braun and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2775 / NOE intraresidue total count: 704 / NOE long range total count: 1333 / NOE medium range total count: 1333 / NOE sequential total count: 738
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 15 / Maximum upper distance constraint violation: 0.39 Å

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