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- PDB-1qey: NMR Structure Determination of the Tetramerization Domain of the ... -

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Basic information

Entry
Database: PDB / ID: 1qey
TitleNMR Structure Determination of the Tetramerization Domain of the MNT Repressor: An Asymmetric A-Helical Assembly in Slow Exchange
ComponentsPROTEIN (REGULATORY PROTEIN MNT)
KeywordsGENE REGULATION / OLIGOMERIZATION / TRANSCRIPTIONAL CONTROL / P22 MNT REPRESSOR
Function / homologyBacteriophage P22, Mnt / Regulatory protein Mnt / Arc-like DNA binding domain / Arc-like DNA binding domain / Arc-type ribbon-helix-helix / Ribbon-helix-helix / regulation of DNA-templated transcription / DNA binding / Regulatory protein mnt
Function and homology information
Biological speciesEnterobacteria phage P22 (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsNooren, I.M.A. / George, A.V.E. / Kaptein, R. / Sauer, R.T. / Boelens, R.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: The tetramerization domain of the Mnt repressor consists of two right-handed coiled coils.
Authors: Nooren, I.M. / Kaptein, R. / Sauer, R.T. / Boelens, R.
#1: Journal: J.Biomol.Nmr / Year: 1999
Title: NMR structure determination of the tetramerization domain of the Mnt repressor: An asymmetric alpha-helical assembly in slow exchange.
Authors: Nooren, I.M. / George, A.V. / Kaptein, R. / Sauer, R.T. / Boelens, R.
#2: Journal: J.Biomol.Struct.Dyn. / Year: 2000
Title: Structure and dynamics of the tetrameric mnt repressor and a model for its DNA complex.
Authors: Nooren, I.M. / Folkers, G.E. / Kaptein, R. / Sauer, R.T. / Boelens, R.
#3: Journal: Biochemistry / Year: 1995
Title: Domains of Mnt repressor: roles in tetramer formation, protein stability, and operator DNA binding.
Authors: Waldburger, C.D. / Sauer, R.T.
History
DepositionApr 3, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Aug 18, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.book_publisher / _citation.country ..._citation.book_publisher / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (REGULATORY PROTEIN MNT)
B: PROTEIN (REGULATORY PROTEIN MNT)
C: PROTEIN (REGULATORY PROTEIN MNT)
D: PROTEIN (REGULATORY PROTEIN MNT)


Theoretical massNumber of molelcules
Total (without water)14,7734
Polymers14,7734
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5270 Å2
ΔGint-62 kcal/mol
Surface area8080 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)27 / 30LOWEST ENERGY, LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein/peptide
PROTEIN (REGULATORY PROTEIN MNT) / MNT-C


Mass: 3693.208 Da / Num. of mol.: 4 / Fragment: C-TERMINAL TETRAMERIZATION DOMAIN
Source method: isolated from a genetically manipulated source
Details: CHYMOTRYPTIC FRAGMENT OF WILD-TYPE PROTEIN / Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / Plasmid: PTM203-ST6 / Production host: Escherichia coli (E. coli) / Strain (production host): X90 / References: UniProt: P03049

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionsIonic strength: 50 mM KPI, 200 mM NACL / pH: 5.2 / Temperature: 298.0 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
Field strength (MHz)Spectrometer-ID
6001
7502

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORV3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: SEE LITERATURE
NMR ensembleConformer selection criteria: LOWEST ENERGY, LEAST RESTRAINT VIOLATION
Conformers calculated total number: 30 / Conformers submitted total number: 27

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