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- PDB-5wqz: Solution structure of a histone binding domain -

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Basic information

Entry
Database: PDB / ID: 5wqz
TitleSolution structure of a histone binding domain
ComponentsPutative uncharacterized protein
KeywordsPROTEIN BINDING / HISTONE BINDING DOMAIN
Function / homologylysine-acetylated histone binding / Bromodomain / Bromodomain / Bromodomain-like superfamily / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / Bromo domain-containing protein
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsMi, J.
CitationJournal: To Be Published
Title: Solution Structure Of A Histone Binding Domain
Authors: Mi, J.
History
DepositionNov 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_database_status / pdbx_nmr_ensemble / pdbx_nmr_refine / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_refine.method / _pdbx_nmr_spectrometer.manufacturer
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: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,8791
Polymers13,8791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative uncharacterized protein / BDF5


Mass: 13878.720 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb11.01.5000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q382J7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
131isotropic13D CBCA(CO)NH
141isotropic13D HBHA(CO)NH
151isotropic13D H(CCO)NH
161isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.5 g/L [U-100% 15N] NH4Cl, 2.5 g/L [U-100% 13C] C6H12O6, 90% H2O/10% D2O
Label: 15N_sample 13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 g/LNH4Cl[U-100% 15N]1
2.5 g/LC6H12O6[U-100% 13C]1
Sample conditionsDetails: 25mM NaH2PO4 100mM Nacl 1mM EDTA 1mM DTT / Ionic strength: 0.8 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR softwareName: CYANA / Developer: GUNTERT, MUMENTHALER AND WUTHRICH / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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