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- PDB-1t23: NMR Solution Structure of the Archaebacterial Chromosomal Protein MC1 -

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Basic information

Entry
Database: PDB / ID: 1t23
TitleNMR Solution Structure of the Archaebacterial Chromosomal Protein MC1
ComponentsChromosomal protein MC1
KeywordsDNA BINDING PROTEIN / alpha/beta barrel
Function / homology
Function and homology information


DNA protection / DNA binding
Similarity search - Function
chromosomal protein mc1 / Chromosomal protein MC1 / Chromosomal protein MC1 / Chromosomal protein MC1 superfamily / Non-histone chromosomal protein MC1 / Roll / Alpha Beta
Similarity search - Domain/homology
Chromosomal protein MC1
Similarity search - Component
Biological speciesMethanosarcina thermophila (archaea)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsPaquet, F. / Culard, F. / Barbault, F. / Maurizot, J.C. / Lancelot, G.
CitationJournal: Biochemistry / Year: 2004
Title: NMR Solution Structure of the Archaebacterial Chromosomal Protein MC1 Reveals a New Protein Fold
Authors: Paquet, F. / Culard, F. / Barbault, F. / Maurizot, J.C. / Lancelot, G.
History
DepositionApr 20, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionDec 7, 2004ID: 1KOM
Revision 1.0Dec 7, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Chromosomal protein MC1


Theoretical massNumber of molelcules
Total (without water)10,6871
Polymers10,6871
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)8 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Chromosomal protein MC1


Mass: 10687.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina thermophila (archaea) / Strain: CHTI55 / References: UniProt: P12770

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using 2D homonuclear spectra

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Sample preparation

DetailsContents: 1.74 mM MC1, 70 mM sodium acetate buffer, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 800mM NaCl / pH: 5.3 / Pressure: ambient / Temperature: 300 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
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVarianprocessing
UXNMRBrukerprocessing
DYANA1.5Guentertstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 8

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