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- PDB-2mw2: Hha-H-NS46 charge zipper complex -

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Basic information

Entry
Database: PDB / ID: 2mw2
TitleHha-H-NS46 charge zipper complex
Components
  • DNA-binding protein H-NS
  • Hemolysin expression-modulating protein Hha
KeywordsDNA BINDING PROTEIN / Nucleoid-associated Proteins / Charge-zipper complex / Electrostatic-driven function / Salt-dependent dynamics
Function / homology
Function and homology information


H-NS-Cnu complex / H-NS complex / H-NS-Hha complex / negative regulation of single-species biofilm formation on inanimate substrate / bacterial nucleoid packaging / bent DNA binding / DNA-binding transcription repressor activity / minor groove of adenine-thymine-rich DNA binding / protein-DNA complex / structural constituent of chromatin ...H-NS-Cnu complex / H-NS complex / H-NS-Hha complex / negative regulation of single-species biofilm formation on inanimate substrate / bacterial nucleoid packaging / bent DNA binding / DNA-binding transcription repressor activity / minor groove of adenine-thymine-rich DNA binding / protein-DNA complex / structural constituent of chromatin / regulation of translation / regulation of gene expression / transcription regulator complex / protein dimerization activity / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / RNA binding / membrane / identical protein binding / cytosol
Similarity search - Function
HHA / Haemolysin expression modulating, HHA / HHA superfamily / Haemolysin expression modulating protein / H-NS histone-like proteins / Histone-like protein H-NS, N-terminal / Histone-like protein H-NS, C-terminal domain superfamily / Histone-like protein H-NS / Histone-like protein H-NS, C-terminal domain / H-NS histone family ...HHA / Haemolysin expression modulating, HHA / HHA superfamily / Haemolysin expression modulating protein / H-NS histone-like proteins / Histone-like protein H-NS, N-terminal / Histone-like protein H-NS, C-terminal domain superfamily / Histone-like protein H-NS / Histone-like protein H-NS, C-terminal domain / H-NS histone family / Domain in histone-like proteins of HNS family / Monooxygenase / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Hemolysin expression-modulating protein Hha / DNA-binding protein H-NS
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodSOLUTION NMR / Rigid-body, torsion angle simulated annealing, Cartesian Molecular dynamics
Model detailslowest energy, model9
AuthorsCordeiro, T.N. / Garcia, J. / Bernado, P. / Millet, O. / Pons, M.
CitationJournal: J. Biol. Chem. / Year: 2015
Title: A Three-protein Charge Zipper Stabilizes a Complex Modulating Bacterial Gene Silencing.
Authors: Cordeiro, T.N. / Garcia, J. / Bernado, P. / Millet, O. / Pons, M.
History
DepositionOct 24, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Structure summary
Revision 1.2Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemolysin expression-modulating protein Hha
B: DNA-binding protein H-NS
C: DNA-binding protein H-NS


Theoretical massNumber of molelcules
Total (without water)19,5763
Polymers19,5763
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)10 / 400target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Hemolysin expression-modulating protein Hha


Mass: 8642.016 Da / Num. of mol.: 1 / Fragment: Residues 1-72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: hha, b0460, JW0449 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACE3
#2: Protein/peptide DNA-binding protein H-NS / Histone-like protein HLP-II / Protein B1 / Protein H1


Mass: 5467.234 Da / Num. of mol.: 2 / Fragment: Residues 1-46
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12
Gene: hns, bglY, cur, drdX, hnsA, msyA, osmZ, pilG, topS, b1237, JW1225
Production host: Escherichia coli (E. coli) / References: UniProt: P0ACF8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
2332D 1H-15N HSQC
2433D 1H-15N NOESY
2533D 1H-15N TOCSY
2642D 1H-15N HSQC
2743D 1H-15N NOESY
2843D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.015-0.030 mM protein_1, 0.10 mM [U-100% 15N] protein_2, 20 mM HEPES, 150 mM sodium chloride, 0.01 w/v sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.015-0.030 mM protein_1, 0.10 mM [U-100% 15N] protein_2, 20 mM HEPES, 150 mM sodium chloride, 0.01 w/v sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.9 mM [U-100% 15N] protein_1, 150 mM sodium chloride, 0.01 w/v sodium azide, 20 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
40.9 mM [U-100% 15N] protein_2, 150 mM sodium chloride, 0.01 w/v sodium azide, 20 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-10.015-0.0301
0.10 mMentity_2-2[U-100% 15N]1
20 mMHEPES-31
150 mMsodium chloride-41
0.01 w/vsodium azide-51
mMentity_1-60.015-0.0302
0.10 mMentity_2-7[U-100% 15N]2
20 mMHEPES-82
150 mMsodium chloride-92
0.01 w/vsodium azide-102
0.9 mMentity_1-11[U-100% 15N]3
150 mMsodium chloride-123
0.01 w/vsodium azide-133
20 mMsodium phosphate-143
0.9 mMentity_2-15[U-100% 15N]4
150 mMsodium chloride-164
0.01 w/vsodium azide-174
20 mMsodium phosphate-184
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.16 7.0 ambient 295 K
20.20 7.0 ambient 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker Avance IIIBrukerAvance III6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Zhengrong and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
CARAKeller and Wuthrichchemical shift assignment
CNS2Brunger, Adams, Clore, Gros, Nilges and Readcalculation engine
Haddock2.1Alexandre Bonvindata-driven docking using cns as structure calculation engine
TOPSPINBruker Biospinnmr spectra acquisition
Haddock2.1Alexandre Bonvinrefinement
CNS2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: Rigid-body, torsion angle simulated annealing, Cartesian Molecular dynamics
Software ordinal: 1
Details: HADDOCK modelling consists of (i) rigid-body docking, (ii) semi-flexible refinement stage and (iii) final refinement in explicit solvent., Final gentle water simulated annealing refinement ...Details: HADDOCK modelling consists of (i) rigid-body docking, (ii) semi-flexible refinement stage and (iii) final refinement in explicit solvent., Final gentle water simulated annealing refinement protocol using molecular dynamics in Cartesian space.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 10

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