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- PDB-2k9s: Solution structure of dna binding domain of E. coli arac -

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Basic information

Entry
Database: PDB / ID: 2k9s
TitleSolution structure of dna binding domain of E. coli arac
ComponentsArabinose operon regulatory protein
KeywordsTRANSCRIPTION / Activator / Arabinose catabolism / Carbohydrate metabolism / Cytoplasm / DNA-binding / Repressor / Transcription regulation
Function / homology
Function and homology information


arabinose catabolic process / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / identical protein binding / cytosol
Similarity search - Function
Transcription regulator HTH-like / AraC-type arabinose-binding/dimerisation domain / AraC-like ligand binding domain / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein ...Transcription regulator HTH-like / AraC-type arabinose-binding/dimerisation domain / AraC-like ligand binding domain / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Arabinose operon regulatory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRodgers, M.E. / Schleif, R.F.
CitationJournal: Proteins / Year: 2009
Title: Solution structure of the DNA binding domain of AraC protein.
Authors: Rodgers, M.E. / Schleif, R.
History
DepositionOct 23, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_spectrometer ...pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 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: Arabinose operon regulatory protein


Theoretical massNumber of molelcules
Total (without water)12,0971
Polymers12,0971
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Arabinose operon regulatory protein


Mass: 12096.711 Da / Num. of mol.: 1 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: araC, b0064, JW0063 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A9E0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 13C-SEPARATED ALI NOESY
1223D 13C-SEPARATED ARO NOESY
1313D 1H-15N-SEPARATED NOESY
1412D 1H-15N HSQC
1522D 1H-13C HSQC
1623D HNCO
1723D HNCA
1823D HN(CA)CB
1923D HN(CO)CA
11023D CBCA(CO)NH
11123D (H)CCH-COSY
11223D (H)CC(CO)NH-TOCSY
11323D H CC(CO)NH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.0 mM [U-100% 15N] AraC-DBD, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1.0 mM [U-100% 13C; U-100% 15N] AraC-DBD, 100% D2O100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMAraC-DBD[U-100% 15N]0.5-1.01
mMAraC-DBD[U-100% 13C; U-100% 15N]0.5-1.02
Sample conditionsIonic strength: 400 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
VARIAN INOVAVarianINOVA8001
Bruker AvanceBrukerAVANCE6002
Varian INOVAVarianINOVA5003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2P.GUNTERT ET AL.refinement
ATNOS-CANDIDHerrmann, Guntert and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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