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- PDB-1wz6: Solution Structure of the HMG_box Domain of Murine Bobby Sox Homolog -

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Basic information

Entry
Database: PDB / ID: 1wz6
TitleSolution Structure of the HMG_box Domain of Murine Bobby Sox Homolog
ComponentsHMG-BOX transcription factor BBX
KeywordsTRANSCRIPTION / bobby sox homolog / transcription factor / HMG_box domain / structural genomics / NPPSFA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


RNA polymerase II transcription regulatory region sequence-specific DNA binding / bone development / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
HMG box transcription factor BBX, domain of unknown function DUF2028 / : / Domain of unknown function (DUF2028) / : / High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain ...HMG box transcription factor BBX, domain of unknown function DUF2028 / : / Domain of unknown function (DUF2028) / : / High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HMG box transcription factor BBX / HMG box transcription factor BBX
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLi, H. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of the HMG_box Domain of Murine Bobby Sox Homolog
Authors: Li, H. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionFeb 25, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2005Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: 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: HMG-BOX transcription factor BBX


Theoretical massNumber of molelcules
Total (without water)9,2901
Polymers9,2901
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)20 / 100target function,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein HMG-BOX transcription factor BBX / Bobby sox homolog


Mass: 9289.592 Da / Num. of mol.: 1 / Fragment: HMG_box domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: Bbx / Plasmid: P040719-04 / References: UniProt: Q8CDV1, UniProt: Q8VBW5*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.55mM HMG_box domain U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.913Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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