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- PDB-2l7z: NMR Structure of A13 homedomain -

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Basic information

Entry
Database: PDB / ID: 2l7z
TitleNMR Structure of A13 homedomain
ComponentsHomeobox protein Hox-A13
KeywordsGENE REGULATION / HOXA13
Function / homology
Function and homology information


chromatin => GO:0000785 / intermediate filament cytoskeleton / skeletal system development / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA binding / nucleoplasm / cytosol
Similarity search - Function
Homeobox protein Hox1A3 N-terminal / Hox protein A13 N terminal / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily ...Homeobox protein Hox1A3 N-terminal / Hox protein A13 N terminal / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Homeobox protein Hox-A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsAmes, J.
CitationJournal: Plos One / Year: 2011
Title: Structural basis for sequence specific DNA binding and protein dimerization of HOXA13.
Authors: Zhang, Y. / Larsen, C.A. / Stadler, H.S. / Ames, J.B.
History
DepositionDec 27, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homeobox protein Hox-A13


Theoretical massNumber of molelcules
Total (without water)8,8881
Polymers8,8881
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 30structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Homeobox protein Hox-A13 / / Homeobox protein Hox-1J


Mass: 8888.468 Da / Num. of mol.: 1 / Fragment: Homeobox domain residues 322-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HOXA13, HOX1J / Production host: Escherichia coli (E. coli) / References: UniProt: P31271

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D HBHA(CO)NH
1513D CBCA(CO)NH

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Sample preparation

DetailsContents: 0.5 mM [U-98% 13C; U-98% 15N] A13, 95 % H2O, 5 % D2O, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMA13-1[U-98% 13C; U-98% 15N]1
95 %H2O-21
5 %D2O-31
Sample conditionsIonic strength: 0.02 / pH: 7.0 / Pressure: 1.0 atm / Temperature: 285 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
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XPLOR-NIHBRUNGER,SCHWIETERS,KUSZEWSKI,TJANDRA,CLORErefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 15

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