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- PDB-1ub1: Solution structure of the matrix attachment region-binding domain... -

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Basic information

Entry
Database: PDB / ID: 1ub1
TitleSolution structure of the matrix attachment region-binding domain of chicken MeCP2
Componentsattachment region binding protein
KeywordsTRANSCRIPTION / Chicken methyl-CpG-binding protein 2 (cMeCP2) / MAR-binding protein (ARBP) / NMR spectroscopy / protein-DNA interaction / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


double-stranded methylated DNA binding / methyl-CpG binding / heterochromatin / chromatin binding / negative regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Methyl-cpg-binding Protein 2; Chain A / Methyl-cpg-binding Protein 2; Chain A / Methyl-CpG binding protein MeCP2/MBD4 / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Attachment region binding protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHeitmann, B. / Maurer, T. / Weitzel, J.M. / Stratling, W.H. / Kalbitzer, H.R. / Brunner, E. / Structural Proteomics in Europe (SPINE)
CitationJournal: EUR.J.BIOCHEM. / Year: 2003
Title: Solution structure of the matrix attachment region-binding domain of chicken MeCP2
Authors: Heitmann, B. / Maurer, T. / Weitzel, J.M. / Stratling, W.H. / Kalbitzer, H.R. / Brunner, E.
History
DepositionMar 27, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX Determination method: author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: attachment region binding protein


Theoretical massNumber of molelcules
Total (without water)14,8171
Polymers14,8171
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)10 / 240target function
Representative

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Components

#1: Protein attachment region binding protein / MeCP2


Mass: 14816.737 Da / Num. of mol.: 1 / Fragment: matrix attachment region-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET-cARBP-Ex4.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: O42403

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1313D 15N-separated NOESY
1423D 13C-separated NOESY
151
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2mM cMeCP2 MAR-BD, U-15N, 13C: 154mM NaCl, 10mM sodium phosphate95% H2O/5% D2O
21-2mM cMeCP2 MAR-BD, U-15N, 13C: 154mM NaCl, 10mM sodium phosphate100% D2O
Sample conditionsIonic strength: 154mM NaCl, 10mM sodium phosphate / pH: 6.8 / Pressure: 1 bar / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker, Karlsruhe, Germanycollection
AURELIANeidig, K.-P.data analysis
AUREMOL1Gronwald, W.data analysis
DYANA1.5Guentert, P.refinement
TALOSCornilescu, G.data analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 240 / Conformers submitted total number: 10

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