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- PDB-1cjg: NMR STRUCTURE OF LAC REPRESSOR HP62-DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1cjg
TitleNMR STRUCTURE OF LAC REPRESSOR HP62-DNA COMPLEX
Components
  • DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3')
  • PROTEIN (LAC REPRESSOR)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / LAC OPERON / LAC REPRESSOR / HEADPIECE / LAC OPERATOR / 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
Transcriptional regulator LacI/GalR-like, sensor domain / LacI-type HTH domain signature. / 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 ...Transcriptional regulator LacI/GalR-like, sensor domain / LacI-type HTH domain signature. / 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 MD
AuthorsSpronk, C.A.E.M. / Bonvin, A.M.J.J. / Radha, P.K. / Melacini, G. / Boelens, R. / Kaptein, R.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: The solution structure of Lac repressor headpiece 62 complexed to a symmetrical lac operator.
Authors: Spronk, C.A. / Bonvin, A.M. / Radha, P.K. / Melacini, G. / Boelens, R. / Kaptein, R.
#1: Journal: Biochemistry / Year: 1997
Title: Backbone and side chain dynamics of lac repressor headpiece (1-56) and its complex with DNA.
Authors: Slijper, M. / Boelens, R. / Davis, A.L. / Konings, R.N. / van der Marel, G.A. / van Boom, J.H. / Kaptein, R.
#2: Journal: Nat.Struct.Biol. / Year: 1996
Title: Formation of the hinge helix in the lac repressor is induced upon binding to the lac operator.
Authors: Spronk, C.A. / Slijper, M. / van Boom, J.H. / Kaptein, R. / Boelens, R.
#3: Journal: J.Mol.Biol. / Year: 1996
Title: Refined structure of lac repressor headpiece (1-56) determined by relaxation matrix calculations from 2D and 3D NOE data: change of tertiary structure upon binding to the lac operator.
Authors: Slijper, M. / Bonvin, A.M. / Boelens, R. / Kaptein, R.
#4: Journal: J.Mol.Biol. / Year: 1993
Title: Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics.
Authors: Chuprina, V.P. / Rullmann, J.A. / Lamerichs, R.M. / van Boom, J.H. / Boelens, R. / Kaptein, R.
History
DepositionApr 14, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.twist
Revision 1.4Dec 27, 2023Group: 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

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Assembly

Deposited unit
C: DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3')
D: DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3')
A: PROTEIN (LAC REPRESSOR)
B: PROTEIN (LAC REPRESSOR)


Theoretical massNumber of molelcules
Total (without water)27,1404
Polymers27,1404
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6080 Å2
ΔGint-39 kcal/mol
Surface area14720 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 14SEE ARTICLE
Representative

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Components

#1: DNA chain DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3') / SYML OPERATOR


Mass: 6751.377 Da / Num. of mol.: 2 / Fragment: SYMMETRIC LAC OPERATOR / Source method: obtained synthetically
Details: THE FRAGMENT IS A VARIANT OF THE WILD-TYPE OPERATOR SEQUENCE OF THE LAC OPERON OF ESCHERICHIA COLI
Keywords: TIGHT BINDING SYMMETRIC OPERATOR
#2: Protein PROTEIN (LAC REPRESSOR) / LAC HP62


Mass: 6818.743 Da / Num. of mol.: 2 / Fragment: HEADPIECE, RESIDUES 1 - 62
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CONTAINS THE 62 N-TERMINAL RESIDUES (I.E., THE DNA BINDING REGION) OF THE COMPLETE LAC REPRESSOR PROTEIN
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: LAC I, THE PART ENCODING THE 62 N-TERMINAL AMINOACIDS / Plasmid: PGP1-2;PET-HP62 / 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 experimentType: SEE ARTICLE
NMR detailsText: RESONANCE ASSIGNMENTS WERE BASED ON VARIOUS HOMONUCLEAR AND DOUBLE AND TRIPLE RESONANCE NMR EXPERIMENTS IN H2O/D2O (95%/5%) AND D2O. IN ADDITION ISOTOPE FILTER EXPERIMENTS WERE APPLIED TO ...Text: RESONANCE ASSIGNMENTS WERE BASED ON VARIOUS HOMONUCLEAR AND DOUBLE AND TRIPLE RESONANCE NMR EXPERIMENTS IN H2O/D2O (95%/5%) AND D2O. 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: SEE ARTICLE
Sample conditionsIonic strength: SEE ARTICLE / pH: 6.1 / Pressure: 1 atm / Temperature: 315 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
Field strength (MHz)Spectrometer-ID
5001
6002
7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851structure solution
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MD / Software ordinal: 1
Details: THE STRUCTURES WERE DETERMINED BY FIRST CALCULATING THE STRUCTURE OF THE HP62 MONOMER USING THE STANDARD XPLOR PARAMETER SETS FOR NMR STRUCTURE DETERMINATION. THE HP62 MONOMERS WERE ...Details: THE STRUCTURES WERE DETERMINED BY FIRST CALCULATING THE STRUCTURE OF THE HP62 MONOMER USING THE STANDARD XPLOR PARAMETER SETS FOR NMR STRUCTURE DETERMINATION. THE HP62 MONOMERS WERE SUBSEQUENTLY DUPLICATED AND DOCKED ONTO A B-DNA TEMPLATE STRUCTURE OF THE LAC OPERATOR, WHICH WAS ALLOWED TO BEND IN ORDER TO ACCOMODATE THE TWO HP62 MONOMERS. THE PROPERLY DOCKED STRUCTURES WERE PLACED IN A TIP3P WATERBOX WHICH WAS NEUTRALIZED BY ADDITION OF SODIUM-IONS. THE STRUCTURES WERE THEN FURTHER REFINED BY A RESTRAINED MD SIMULATION OF 24 PS IN THE CHARMM22 FORCEFIELD FOR PROTEINS AND NUCLEIC ACIDS. NCS SYMMETRY RESTRAINTS WERE USED DURING THE DOCKING AND REFINEMENT PROCEDURES. FOR FURTHER REFINEMENT DETAILS SEE THE PAPER DESCRIBING THE STRUCTURES
NMR ensembleConformer selection criteria: SEE ARTICLE / Conformers calculated total number: 14 / Conformers submitted total number: 11

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