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- PDB-5ogu: Structure of DNA-binding HU protein from micoplasma Spiroplasma m... -

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Basic information

Entry
Database: PDB / ID: 5ogu
TitleStructure of DNA-binding HU protein from micoplasma Spiroplasma melliferum
ComponentsDNA-binding protein
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


structural constituent of chromatin / DNA binding
Similarity search - Function
HU Protein; Chain A / IHF-like DNA-binding proteins / Histone-like DNA-binding protein, conserved site / Bacterial histone-like DNA-binding proteins signature. / 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
Biological speciesSpiroplasma melliferum KC3 (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsAltukhov, D.A. / Talyzina, A.A. / Agapova, Y.K. / Vlaskina, A.V. / Korzhenevskiy, D.A. / Bocharov, E.V. / Rakitina, T.V. / Timofeev, V.I.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation15-14-00063 Russian Federation
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2018
Title: Structural plasticity and thermal stability of the histone-like protein from Spiroplasma melliferum are due to phenylalanine insertions into the conservative scaffold.
Authors: Timofeev, V.I. / Altukhov, D.A. / Talyzina, A.A. / Agapova, Y.K. / Vlaskina, A.V. / Korzhenevskiy, D.A. / Kleymenov, S.Y. / Bocharov, E.V. / Rakitina, T.V.
History
DepositionJul 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Nov 9, 2022Group: Database references / Category: citation / citation_author / 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 1.3Jun 19, 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: DNA-binding protein
B: DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)20,5842
Polymers20,5842
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4600 Å2
ΔGint-42 kcal/mol
Surface area11830 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 5000structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA-binding protein


Mass: 10291.794 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spiroplasma melliferum KC3 (bacteria) / Gene: SPM_000560 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A037USE5

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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
121isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 5 % [U-2H] D2O, 95% H2O/5% D2O / Label: sample_1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 5 % / Component: D2O / Isotopic labeling: [U-2H]
Sample conditionsIonic strength: 0.375 M / Label: conditions_1 / pH: 6.7 Not defined / Pressure: 1 atm / Temperature: 303 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
GROMACSHerman Berendsen's group, department of Biophysical Chemistry of Groningen Universityrefinement
TALOS+Cornilescu, Delaglio and Baxchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 5000 / Conformers submitted total number: 15

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