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- PDB-1l1m: SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN... -

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Basic information

Entry
Database: PDB / ID: 1l1m
TitleSOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN COMPLEXED TO ITS NATURAL OPERATOR O1
Components
  • 5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3'
  • 5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP*AP*TP*TP*T)-3'
  • Lactose operon repressor
KeywordsTRANSCRIPTION REGULATOR/DNA / TRANSCRIPTION REGULATION / LAC OPERON / LAC REPRESSOR / NATURAL LAC OPERATOR / ASYMMETRIC DNA-BINDING / HTH / TRANSCRIPTION REGULATOR-DNA COMPLEX
Function / homology
Function and homology information


DNA-binding transcription repressor activity / cis-regulatory region sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily ...LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Periplasmic binding protein-like I / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Lactose operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MDR
AuthorsKalodimos, C.G. / Bonvin, A.M.J.J. / Salinas, R.K. / Wechselberger, R. / Boelens, R. / Kaptein, R.
Citation
Journal: EMBO J. / Year: 2002
Title: Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain.
Authors: Kalodimos, C.G. / Bonvin, A.M. / Salinas, R.K. / Wechselberger, R. / Boelens, R. / Kaptein, R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Strong DNA binding by covalently linked dimeric lac headpiece: evidence for the crucial role of the hinge helices
Authors: Kalodimos, C.G. / Folkers, G. / Boelens, R. / Kaptein, R.
History
DepositionFeb 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP*AP*TP*TP*T)-3'
D: 5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3'
A: Lactose operon repressor
B: Lactose operon repressor


Theoretical massNumber of molelcules
Total (without water)27,7644
Polymers27,7644
Non-polymers00
Water00
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 lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain 5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP*AP*TP*TP*T)-3'


Mass: 7143.645 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Lac operator O1; this is the wild-type operator sequence of the lac operon in E. coli.
#2: DNA chain 5'-D(*AP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3'


Mass: 6974.534 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Lac operator O1; this is the wild-type operator sequence of the lac operon in E. coli.
#3: Protein Lactose operon repressor


Mass: 6822.755 Da / Num. of mol.: 2 / Fragment: N-terminal DNA-binding domain, Residues 1-62 / Mutation: V52C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: LACI / Plasmid: PGP1-2,PET-HP62 / Production host: Escherichia coli (E. coli) / Strain (production host): DH9 / References: UniProt: P03023
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1312D NOESY
NMR detailsText: This structure was determined using standard 2D and 3D homo- and heteronuclearnuclear techniques. 13C-15N labeled protein was used and unlabeled nucleotide. IN ADDITION ISOTOPE FILTER ...Text: This structure was determined using standard 2D and 3D homo- and heteronuclearnuclear techniques. 13C-15N labeled protein was used and unlabeled nucleotide. IN ADDITION ISOTOPE FILTER EXPERIMENTS WERE APPLIED TO OBTAIN ADDITIONAL ASSIGNMENTS AND TO ASSIGN INTER-MOLECULAR NOES. FOR FURTHER DETAILS SEE THE REFERENCE DESCRIBING THE STRUCTURES.

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Sample preparation

DetailsContents: 2mM Lac-HP62-V52C U-15N,13C, 10mM KPi, 20mM KCl, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10mM KPi, 20mM KCl / pH: 6 / Pressure: ambient / Temperature: 315 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX7501
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
NMRPipe1Delaglioprocessing
NMRView5.0.4Johnsondata analysis
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MDR / Software ordinal: 1
Details: The structure of the complex was calculated as follows. First the structure of the dimeric lac HP62-V52C was calculated using only protein NMR restraints. The 50 best structures were ...Details: The structure of the complex was calculated as follows. First the structure of the dimeric lac HP62-V52C was calculated using only protein NMR restraints. The 50 best structures were selected and docked onto the natural lac operator B-DNA using simulated annealing. Distance and planarity restraints for the DNA were incorporated in order to keep DNA close to B-DNA but allowing a bend necessary to accommodate the two headpiece molecules on the DNA.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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