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- PDB-2l4a: NMR structure of the DNA-binding domain of E.coli Lrp -

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Basic information

Entry
Database: PDB / ID: 2l4a
TitleNMR structure of the DNA-binding domain of E.coli Lrp
ComponentsLeucine responsive regulatory protein
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


alanine catabolic process / response to L-leucine / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
Transcription regulator HTH, AsnC-type, conserved site / AsnC-type HTH domain signature. / AsnC-type HTH domain profile. / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding / ArsR-like helix-turn-helix domain ...Transcription regulator HTH, AsnC-type, conserved site / AsnC-type HTH domain signature. / AsnC-type HTH domain profile. / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Leucine-responsive regulatory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailsminimized average, model 1
AuthorsKawamura, T. / Zhou, H. / Dahlquist, F.W.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The design involved in PapI and Lrp regulation of the pap operon.
Authors: Kawamura, T. / Vartanian, A.S. / Zhou, H. / Dahlquist, F.W.
History
DepositionOct 1, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine responsive regulatory protein


Theoretical massNumber of molelcules
Total (without water)7,6221
Polymers7,6221
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)26 / 100minimized average structure and 25 structures with the lowest energy
RepresentativeModel #1minimized average

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Components

#1: Protein Leucine responsive regulatory protein


Mass: 7621.809 Da / Num. of mol.: 1 / Fragment: unp residues 1-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lrp / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5CYP4, UniProt: P0ACJ0*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: 25 calculated results and the averaged/minimized structure
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D (H)CCH-TOCSY
1613D HN(CA)CB
1714D 15N-13C edited NOESY
2824D 13C-131C edited NOESY
3932D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-99% 13C; U-99% 15N] Lrp DNA-binding domain, 50 mM potassium phosphate, 5 mM beta-mercaptoethanol, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-99% 13C; U-99% 15N] Lrp DNA-binding domian, 50 mM potassium phosphate, 2 mM DTT, 100% D2O100% D2O
380-150 uM [U-99% 13C; U-99% 15N] Lrp DNA-biinding domain, 30 mM potassium phosphate, 2 mM beta-mercaptoethanol, 20 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
2 mMLrp DNA-binding domain-1[U-99% 13C; U-99% 15N]1
50 mMpotassium phosphate-21
5 mMbeta-mercaptoethanol-31
2 mMLrp DNA-binding domian-4[U-99% 13C; U-99% 15N]2
50 mMpotassium phosphate-52
2 mMDTT-62
uMLrp DNA-biinding domain-7[U-99% 13C; U-99% 15N]80-1503
30 mMpotassium phosphate-83
2 mMbeta-mercaptoethanol-93
20 mMpotassium chloride-103
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.05 6.5 ambient 298 K
20.05 6.5 ambient 298 K
30.05 6.5 ambient 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ANSIG3.3Kraulischemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
X-PLORBrungerstructure solution
X-PLORBrungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: minimized average structure and 25 structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 26

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