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- PDB-2lyp: NOE-based 3D structure of the monomer of CylR2 in equilibrium wit... -

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Basic information

Entry
Database: PDB / ID: 2lyp
TitleNOE-based 3D structure of the monomer of CylR2 in equilibrium with predissociated homodimer at 266K (-7 Celsius degrees)
ComponentsCylR2
KeywordsDNA BINDING PROTEIN / homodimer / CylR2 / NOE-based structure / protein folding / cold denaturation / cytolysin repressor 2 / helix-turn-helix / ensemble calculations / fast exchange dimer-monomer equlibrium / dimer dissociation
Function / homology
Function and homology information


Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterococcus faecalis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsJaremko, M. / Jaremko, L. / Kim, H. / Cho, M. / Schwieters, C.D. / Giller, K. / Becker, S. / Zweckstetter, M.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Cold denaturation of a protein dimer monitored at atomic resolution.
Authors: Jaremko, M. / Jaremko, L. / Kim, H.Y. / Cho, M.K. / Schwieters, C.D. / Giller, K. / Becker, S. / Zweckstetter, M.
History
DepositionSep 19, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Jun 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 1.4May 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: CylR2


Theoretical massNumber of molelcules
Total (without water)7,7251
Polymers7,7251
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)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein CylR2 / Putative transcription regulator


Mass: 7724.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: cylR2 / Plasmid: PET32A / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q8VL32

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D 1H-15N NOESY
1513D 1H-13C NOESY aliphatic
1613D 1H-13C NOESY aromatic
1713D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.52 mM [U-100% 13C; U-100% 15N] CylR2, 600 mM sodium chloride, 50 mM HEPES, 93 % H2O, 7 % D2O, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.52 mMCylR2-1[U-100% 13C; U-100% 15N]1
600 mMsodium chloride-21
50 mMHEPES-31
93 %H2O-41
7 %D2O-51
Sample conditionsIonic strength: 0.6 / pH: 7 / Pressure: ambient / Temperature: 266 K

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NMR measurement

NMR spectrometerType: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.28Schwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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