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- PDB-2ndp: Structure of DNA-binding HU protein from micoplasma Mycoplasma ga... -

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Basic information

Entry
Database: PDB / ID: 2ndp
TitleStructure of DNA-binding HU protein from micoplasma Mycoplasma gallisepticum
ComponentsHistone-like DNA-binding superfamily protein
KeywordsDNA BINDING PROTEIN / Histone-like protein
Function / homology
Function and homology information


chromosome condensation / structural constituent of chromatin / DNA binding / cytosol
Similarity search - Function
HU Protein; Chain A / IHF-like DNA-binding proteins / Histone-like DNA-binding protein / Bacterial DNA-binding protein / bacterial (prokaryotic) histone like domain / Integration host factor (IHF)-like DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Histone-like DNA-binding superfamily protein
Similarity search - Component
Biological speciesMycoplasma gallisepticum S6 (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsfewest violations, model1
AuthorsAltukhov, D.A. / Talyzina, A.A. / Agapova, Y.K. / Vlaskina, A.V. / Korzhenevskiy, D.A. / Bocharov, E.V. / Rakitina, T.V. / Timofeev, V.I. / Popov, V.O.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2018
Title: Enhanced conformational flexibility of the histone-like (HU) protein from Mycoplasma gallisepticum.
Authors: Altukhov, D.A. / Talyzina, A.A. / Agapova, Y.K. / Vlaskina, A.V. / Korzhenevskiy, D.A. / Bocharov, E.V. / Rakitina, T.V. / Timofeev, V.I. / Popov, V.O.
History
DepositionSep 13, 2016Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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: Histone-like DNA-binding superfamily protein
B: Histone-like DNA-binding superfamily protein


Theoretical massNumber of molelcules
Total (without water)21,9662
Polymers21,9662
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)15 / 5000structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Histone-like DNA-binding superfamily protein


Mass: 10983.087 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma gallisepticum S6 (bacteria) / Strain: S6 / Gene: hup_2, GCW_02335 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6CKR5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC

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Sample preparation

DetailsContents: 5 M [U-2H] D2O-1, 50 mM sodium phosphate-2, 0.1 mM sodium azide-3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 MD2O-1[U-2H]1
50 mMsodium phosphate-21
0.1 mMsodium azide-31
Sample conditionsIonic strength: 0.375 / pH: 6.7 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Agilent Uniform NMR System / Manufacturer: Agilent / Model: Uniform NMR System / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TALOS++Cornilescu, Delaglio and Baxchemical shift assignment
GROMACSHerman Berendsen's group, department of Biophysical Chemistry of Groningen Universityrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 5000 / Conformers submitted total number: 15 / Representative conformer: 1

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