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- PDB-1i11: SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN, SOX-5 HMG BOX FROM MOUSE -

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Entry
Database: PDB / ID: 1i11
TitleSOLUTION STRUCTURE OF THE DNA BINDING DOMAIN, SOX-5 HMG BOX FROM MOUSE
ComponentsTRANSCRIPTION FACTOR SOX-5
KeywordsDNA BINDING PROTEIN / HMG BOX / DNA BENDING / DNA RECOGNITION / CHROMATIN / DNA SEQUENCE SPECIFIC / TESTIS DETERMINING.
Function / homology
Function and homology information


regulation of timing of neuron differentiation / central nervous system neuron differentiation / positive regulation of chondrocyte differentiation / cartilage development / cartilage condensation / oligodendrocyte differentiation / cell fate commitment / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / in utero embryonic development ...regulation of timing of neuron differentiation / central nervous system neuron differentiation / positive regulation of chondrocyte differentiation / cartilage development / cartilage condensation / oligodendrocyte differentiation / cell fate commitment / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / in utero embryonic development / transcription regulator complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / 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
Transcription factor SOX-5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / SIMULATING ANNEALING
AuthorsCary, P.D. / Read, C.M. / Davis, B. / Driscoll, P.C. / Crane-Robinson, C.
CitationJournal: Protein Sci. / Year: 2001
Title: Solution structure and backbone dynamics of the DNA-binding domain of mouse Sox-5.
Authors: Cary, P.D. / Read, C.M. / Davis, B. / Driscoll, P.C. / Crane-Robinson, C.
History
DepositionJan 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample ...database_2 / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.solvent_system / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.manufacturer
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: TRANSCRIPTION FACTOR SOX-5


Theoretical massNumber of molelcules
Total (without water)9,8251
Polymers9,8251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 50structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TRANSCRIPTION FACTOR SOX-5


Mass: 9825.412 Da / Num. of mol.: 1 / Fragment: HMG BOX
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: SOX-5 / Organ: TESTIS / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P35710

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H NOESY
1242D 1H NOESY
1332D 15N-1H HMQC-J
1413D 15N-1H NOESY
NMR detailsText: This Structure was determined using a combination of 2D and 3D NMR spectra. THE 30 STRUCTURES ARE ALIGNED OVER ALL BACKBONE ATOMS FOR RESIDUES 10-25 AND 32-43. MODEL 1 IS THE MINIMUM ENERGY AND ...Text: This Structure was determined using a combination of 2D and 3D NMR spectra. THE 30 STRUCTURES ARE ALIGNED OVER ALL BACKBONE ATOMS FOR RESIDUES 10-25 AND 32-43. MODEL 1 IS THE MINIMUM ENERGY AND REFERENCE STRUCTURE FOR THE OTHER 29 STRUCTURES.

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12-3 mM [U-100% 15N] Sox-5 HMG Box, 75 mM potassium phosphate buffer, 0.5 mM DTT, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution23 mM Sox-5 HMG Box, 75 mM potassium phosphate buffer, 0.5 mM DTT, 100% D2Osample_2100% D2O
solution31 mM [U-100% 15N] Sox-5 HMG Box, 75 mM potassium phosphate buffer, 0.5 mM DTT, 90% H2O/10% D2Osample_390% H2O/10% D2O
solution43 mM Sox-5 HMG Box, 75 mM potassium phosphate buffer, 0.5 mM DTT, 90% H2O/10% D2Osample_490% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMSox-5 HMG Box[U-100% 15N]2-31
75 mMpotassium phosphate buffernatural abundance1
0.5 mMDTTnatural abundance1
3 mMSox-5 HMG Boxnatural abundance2
75 mMpotassium phosphate buffernatural abundance2
0.5 mMDTTnatural abundance2
1 mMSox-5 HMG Box[U-100% 15N]13
75 mMpotassium phosphate buffernatural abundance3
0.5 mMDTTnatural abundance3
3 mMSox-5 HMG Boxnatural abundance4
75 mMpotassium phosphate buffernatural abundance4
0.5 mMDTTnatural abundance4
Sample conditionsIonic strength: 75 mM KPO4 / pH: 6.2 / Pressure: Ambient / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA6001
Bruker AMBrukerAM6002
Varian UNITYPLUSVarianUNITYPLUS5003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
Felix2.3Molecular Simulationsdata analysis
NMRView3JOHNSON, BRUCE A.data analysis
Insight II97Molecular Simulationsdata analysis
RefinementMethod: SIMULATING ANNEALING / Software ordinal: 1
Details: Structures are based on a total of 1383 nonredundant distance NOE restraints, 61 dihedral angle restraints and 24 paired distance restraints for hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 30

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