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- PDB-1g2h: SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN OF THE TYRR PROTEIN ... -

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Basic information

Entry
Database: PDB / ID: 1g2h
TitleSOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN OF THE TYRR PROTEIN OF HAEMOPHILUS INFLUENZAE
ComponentsTRANSCRIPTIONAL REGULATORY PROTEIN TYRR HOMOLOG
KeywordsTRANSCRIPTION / TyrR / protein structure / NMR / DNA-binding domain / helix-turn-helix motif
Function / homology
Function and homology information


: / phosphorelay signal transduction system / transcription factor binding / regulation of DNA-templated transcription / DNA binding / ATP binding / cytoplasm
Similarity search - Function
TyrR family, helix-turn-helix domain / Helix-turn-helix domain / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A ...TyrR family, helix-turn-helix domain / Helix-turn-helix domain / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulatory protein TyrR
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, Y. / Zhao, S. / Somerville, R.L. / Jardetzky, O.
CitationJournal: Protein Sci. / Year: 2001
Title: Solution structure of the DNA-binding domain of the TyrR protein of Haemophilus influenzae.
Authors: Wang, Y. / Zhao, S. / Somerville, R.L. / Jardetzky, O.
History
DepositionOct 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATORY PROTEIN TYRR HOMOLOG


Theoretical massNumber of molelcules
Total (without water)6,8871
Polymers6,8871
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)32 / 100structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein TRANSCRIPTIONAL REGULATORY PROTEIN TYRR HOMOLOG


Mass: 6886.876 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN; RESIDUES 258-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P44694

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121
1312D TOCSY
2423D 15N-separated NOESY
252HMQC-J
NMR detailsText: The structures were determined using standard 2D homonuclear and 3D heteronuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM TyrR(258-318), 50mM phosphate buffer90% H2O/10% D2O
22mM TyrR(258-318), U-15N, 50mM phosphate buffer90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.5 ambient 298 K
26.5 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.5Viarnprocessing
X-PLOR3.85Brungerstructure solution
X-PLOR3.85Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 32

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