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- PDB-2khl: Refined solution structure of Methanosarcina thermophila protein MC1 -

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Basic information

Entry
Database: PDB / ID: 2khl
TitleRefined solution structure of Methanosarcina thermophila protein MC1
ComponentsChromosomal protein MC1
KeywordsDNA BINDING PROTEIN / DNA-binding protein / alpha and beta / DNA-binding
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 / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsPaquet, F. / Meudal, H. / Culard, F. / Lancelot, G.
CitationJournal: Febs J. / Year: 2010
Title: Refined solution structure and backbone dynamics of the archaeal MC1 protein
Authors: Paquet, F. / Loth, K. / Meudal, H. / Culard, F. / Genest, D. / Lancelot, G.
History
DepositionApr 8, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3May 1, 2024Group: 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: 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)15 / 600structures with the lowest energy
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 genetically manipulated source
Source: (gene. exp.) Methanosarcina thermophila (archaea) / Strain: CHTI 55 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P12770

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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
1313D (H)CCH-TOCSY
1413D HN(CO)CA
1513D HNCA
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D HNCO
1922D 1H-15N HSQC
11012D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.6 mM [U-95% 13C; U-95% 15N] MC1-1, 100 mM sodium acetate-2, 800 mM sodium chloride-3, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-95% 13C; U-95% 15N] MC1-4, 100 mM sodium acetate-5, 800 mM sodium chloride-6, 7 % polyacrylamide gel-7, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.6 mMMC1-1[U-95% 13C; U-95% 15N]1
100 mMsodium acetate-21
800 mMsodium chloride-31
0.5 mMMC1-4[U-95% 13C; U-95% 15N]2
100 mMsodium acetate-52
800 mMsodium chloride-62
7 %polyacrylamide gel-72
Sample conditionspH: 5.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Rieping, Habeck, Bardiaux, Bernard, Malliavin and Nilgesstructure solution
ARIA2.2Rieping, Habeck, Bardiaux, Bernard, Malliavin and Nilgesrefinement
NMRPipeLinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.0.16Johnson, One Moon Scientificchemical shift assignment
NMRView5.0.16Johnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 600 / Conformers submitted total number: 15 / Representative conformer: 1

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