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- PDB-2p7c: Solution structure of the bacillus licheniformis BlaI monomeric f... -

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Basic information

Entry
Database: PDB / ID: 2p7c
TitleSolution structure of the bacillus licheniformis BlaI monomeric form in complex with the blaP half-operator.
Components
  • Penicillinase repressor
  • Strand 1 of Twelve base-pair DNA
  • Strand 2 of Twelve base-pair DNA
Keywordstranscription regulator / PROTEIN-DNA COMPLEX / REPRESSOR / MONOMER / OPERATOR / ANTIBIOTICS
Function / homology
Function and homology information


response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
BlaI transcriptional regulatory family / Penicillinase repressor / 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
DNA / DNA (> 10) / Penicillinase repressor
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodSOLUTION NMR / simulated annealing from randomized coordinates, restrained molecular dynamics.
AuthorsBoudet, J. / Duval, V. / Van Melckebeke, H. / Blackledge, M. / Amoroso, A. / Joris, B. / Simorre, J.-P.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Conformational and thermodynamic changes of the repressor/DNA operator complex upon monomerization shed new light on regulation mechanisms of bacterial resistance against beta-lactam antibiotics.
Authors: Boudet, J. / Duval, V. / Van Melckebeke, H. / Blackledge, M. / Amoroso, A. / Joris, B. / Simorre, J.P.
History
DepositionMar 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: Strand 1 of Twelve base-pair DNA
C: Strand 2 of Twelve base-pair DNA
B: Penicillinase repressor


Theoretical massNumber of molelcules
Total (without water)16,8333
Polymers16,8333
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)10 / 250structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain Strand 1 of Twelve base-pair DNA


Mass: 3669.442 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthetized bacillus licheniformis blaP half-operator
#2: DNA chain Strand 2 of Twelve base-pair DNA


Mass: 3651.414 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthetized bacillus licheniformis blaP half-operator
#3: Protein Penicillinase repressor / Regulatory protein blaI / Beta-lactamase repressor protein


Mass: 9512.079 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: bacillus licheniformis 749/I / Gene: blaI, penI / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLys / References: UniProt: P06555

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D isotopically doubly filtered 13C 15N NOESY HSQC
1213D isotopically doubly filtered 13C 15N NOESY HSQC
1322D filtered NOESY
143methyl selective 13C HSQC
15315N HSQC
NMR detailsText: The structure was determined using a de novo docking approach.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM 13C,15N BlaI-NTD repressor in complex with blaP half-operator; 50mM NaH2PO4/Na2HPO4, 200mM KCl, 1mM EDTA, 1mM NaN390% H2O/10% D2O
22mM 13C,15N BlaI-NTD repressor in complex with blaP half-operator; 50mM NaH2PO4/Na2HPO4, 200mM KCl, 1mM EDTA, 1mM NaN3100% D2O
30.1mM 13C,15N BlaI-NTD repressor; 50mM NaH2PO4/Na2HPO4, 200mM KCl, 1mM EDTA, 1mM NaN390% H2O/10% D2O
Sample conditionsIonic strength: 200mM / pH: 7.6 / Pressure: ambient / Temperature: 298 K

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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
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
Discover2.98Accelrysstructure solution
Discover2.98Accelrysrefinement
NMRPipe2.3Delaglioprocessing
VnmrJ2.1Variancollection
NMRView5.2.2Johnsondata analysis
RefinementMethod: simulated annealing from randomized coordinates, restrained molecular dynamics.
Software ordinal: 1
Details: structures used for refinement were generated from the docking procedure started with intermolecular nOe and ambiguous distance restraints proceeding from chemical shift mapping.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 10

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