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- PDB-1osl: Solution structure of a dimeric lactose DNA-binding domain comple... -

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Basic information

Entry
Database: PDB / ID: 1osl
TitleSolution structure of a dimeric lactose DNA-binding domain complexed to a nonspecific DNA sequence
Components
  • 5'-D(*CP*GP*AP*TP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*AP*TP*CP*G)-3'
  • Lactose operon repressor
KeywordsTRANSCRIPTION/DNA / Protein-DNA complex / Lac repressor / nonspecific interaction / TRANSCRIPTION-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 / THE STRUCTURE OF THE COMPLEX WAS CALCULATED AS FOLLOWS. FIRST THE STRUCTURE OF THE DIMERIC LACHP62-V52C WAS CALCULATED USING ONLY PROTEIN NMR RESTRAINTS. THE 100 BEST STRUCTURES WERE SELECTED, DOCKED ONTO THE NONSPECIFIC LAC OPERATOR B-DNA USING SIMULATED ANNEALING. DISTANCE, PLANARITY RESTRAINTS FOR THE DNA WERE INCORPORATED IN ORDER TO KEEP DNA CLOSE TO B-DNA CONFORMATION.
AuthorsKalodimos, C.G. / Bonvin, A.M.J.J. / Boelens, R. / Kaptein, R.
CitationJournal: Science / Year: 2004
Title: Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes.
Authors: Kalodimos, C.G. / Biris, N. / Bonvin, A.M. / Levandoski, M.M. / Guennuegues, M. / Boelens, R. / Kaptein, R.
History
DepositionMar 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*CP*GP*AP*TP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*AP*TP*CP*G)-3'
D: 5'-D(*CP*GP*AP*TP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*AP*TP*CP*G)-3'
A: Lactose operon repressor
B: Lactose operon repressor


Theoretical massNumber of molelcules
Total (without water)24,6754
Polymers24,6754
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 / 400structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain 5'-D(*CP*GP*AP*TP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*AP*TP*CP*G)-3'


Mass: 5514.603 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: 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: PET-HP62-V52C / Production host: Escherichia coli (E. coli) / Strain (production host): DH9 / References: UniProt: P03023

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
13113C-15N double-half NOESY filter
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D AND 3D HOMO- AND HETERONUCLEAR TECHNIQUES. 13C-15N LABELED PROTEIN AND UNLABELED NUCLEOTIDE WERE USED. IN ADDITION ISOTOPE FILTER EXPERIMENTS ...Text: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D AND 3D HOMO- AND HETERONUCLEAR TECHNIQUES. 13C-15N LABELED PROTEIN AND UNLABELED NUCLEOTIDE WERE USED. 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, 60mM KPI, 400mM KCL / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 400mM KCl, 60mM KPi / pH: 5.8 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3brukercollection
NMRPipe2.1delaglioprocessing
NMRView5.0.3Johnsondata analysis
CNS1.1brungerstructure solution
CNS1.1brungerrefinement
RefinementMethod: THE STRUCTURE OF THE COMPLEX WAS CALCULATED AS FOLLOWS. FIRST THE STRUCTURE OF THE DIMERIC LACHP62-V52C WAS CALCULATED USING ONLY PROTEIN NMR RESTRAINTS. THE 100 BEST STRUCTURES WERE ...Method: THE STRUCTURE OF THE COMPLEX WAS CALCULATED AS FOLLOWS. FIRST THE STRUCTURE OF THE DIMERIC LACHP62-V52C WAS CALCULATED USING ONLY PROTEIN NMR RESTRAINTS. THE 100 BEST STRUCTURES WERE SELECTED, DOCKED ONTO THE NONSPECIFIC LAC OPERATOR B-DNA USING SIMULATED ANNEALING. DISTANCE, PLANARITY RESTRAINTS FOR THE DNA WERE INCORPORATED IN ORDER TO KEEP DNA CLOSE TO B-DNA CONFORMATION.
Software ordinal: 1
Details: THE STRUCTURE OF THE COMPLEX WAS SOLVED ON THE BASIS OF 70 INTERMOLECULAR RESTRAINTS
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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