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- PDB-2l66: The DNA-recognition fold of Sso7c4 suggests a new member of SpoVT... -

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Basic information

Entry
Database: PDB / ID: 2l66
TitleThe DNA-recognition fold of Sso7c4 suggests a new member of SpoVT-AbrB superfamily from archaea.
ComponentsTranscriptional regulator, AbrB family
KeywordsTRANSCRIPTION REGULATOR / DNA binding protein
Function / homology
Function and homology information


Pemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #10 / SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Transcriptional regulator, AbrB family
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsHsu, C.-H. / Wang, A.H.-J.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: The DNA-recognition fold of Sso7c4 suggests a new member of SpoVT-AbrB superfamily from archaea.
Authors: Hsu, C.-H. / Wang, A.H.-J.
History
DepositionNov 17, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, AbrB family
B: Transcriptional regulator, AbrB family


Theoretical massNumber of molelcules
Total (without water)12,3042
Polymers12,3042
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 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Transcriptional regulator, AbrB family / Sso7c4


Mass: 6152.181 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: 98/2 / Gene: Ssol_1031 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0KRA5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D DQF-COSY
1222D 1H-1H TOCSY
1322D 1H-1H NOESY
1412D 1H-15N HSQC
1513D 1H-15N NOESY
1613D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-99% 15N] Sso7c4-1, 20 mM potassium phosphate-2, 50 mM sodium chloride-3, 90% H2O/10% D2O90% H2O/10% D2O
21 mM Sso7c4-4, 20 mM potassium phosphate-5, 50 mM sodium chloride-6, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMSso7c4-1[U-99% 15N]1
20 mMpotassium phosphate-21
50 mMsodium chloride-31
1 mMSso7c4-42
20 mMpotassium phosphate-52
50 mMsodium chloride-62
Sample conditionsIonic strength: 0.05 / pH: 5.0 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.2Goddardchemical shift assignment
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 15 / Representative conformer: 1

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