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- PDB-1lcc: STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BAS... -

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Entry
Database: PDB / ID: 1lcc
TitleSTRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BASE-PAIR HALF-OPERATOR DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS
Components
  • DNA (5'-D(*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
  • Lac Repressor
KeywordsGENE REGULATION/DNA / DNA / HALF-OPERATOR / LAC OPERATOR / LAC REPRESSOR / HEADPIECE / GENE REGULATION-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
AuthorsChuprina, V.P. / Rullmann, J.A.C. / Lamerichs, R.M.J.N. / Van Boom, J.H. / Boelens, R. / Kaptein, R.
Citation
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.
#1: Journal: Eur.J.Biochem. / Year: 1990
Title: Assignment of the 1H-NMR Spectrum of a Lac Repressor Headpiece-Operator Complex in H2O and Identification of Noes. Consequences for Protein-DNA Interaction
Authors: Lamerichs, R.M.J.N. / Boelens, R. / Van Der Marel, G.A. / Van Boom, J.H. / Kaptein, R.
#2: Journal: Biochem.Pharm. / Year: 1990
Title: Two-Dimensional NMR Study of a Protein-DNA Complex. Lac Repressor Headpiece-Operator Interaction
Authors: Kaptein, R. / Lamerichs, R.M.J.N. / Boelens, R. / Rullmann, J.A.C.
#3: Journal: Biochemistry / Year: 1989
Title: 1H NMR Study of a Complex between the Lac Repressor Headpiece and a 22 Base Pair Symmetric Lac Operator
Authors: Lamerichs, R.M.J.N. / Boelens, R. / Van Der Marel, G.A. / Van Boom, J.H. / Kaptein, R. / Buck, F. / Fera, B. / Rueterjans, H.
#4: Journal: Ucla Symp.Mol.Cell.Biol., New Ser. / Year: 1989
Title: NMR Based Docking Studies of Lac Repressor Headpiece on a Lac Operator Fragment
Authors: Rullmann, J.A.C. / Boelens, R. / Kaptein, R.
#5: Journal: Protein Seq.Data Anal. / Year: 1988
Title: The Interaction of Lac Repressor Headpiece with its Operator: An NMR View
Authors: Boelens, R. / Lamerichs, R.M.J.N. / Rullmann, J.A.C. / Van Boom, J.H. / Kaptein, R.
#6: Journal: Proteins / Year: 1988
Title: Combined Procedure of Distance Geometry and Restrained Molecular Dynamics Techniques for Protein Structure Determination from Nuclear Magnetic Resonance Data: Application to the DNA Binding ...Title: Combined Procedure of Distance Geometry and Restrained Molecular Dynamics Techniques for Protein Structure Determination from Nuclear Magnetic Resonance Data: Application to the DNA Binding Domain of Lac Repressor from Escherichia Coli
Authors: De Vlieg, J. / Scheek, R.M. / Van Gunsteren, W.F. / Berendsen, H.J.C. / Kaptein, R. / Thomason, J.
#7: Journal: Nato Asi Ser.,Ser.A / Year: 1987
Title: A Two-Dimensional NMR Study of the Complex of Lac Repressor Headpiece with a 14 Base Pair Lac Operator Fragment
Authors: Boelens, R. / Scheek, R.M. / Lamerichs, R.M.J.N. / De Vlieg, J. / Van Boom, J.H. / Kaptein, R.
#8: Journal: J.Mol.Biol. / Year: 1987
Title: Complex of Lac Repressor Headpiece with a 14 Base Pair Lac Operator Fragment Studied by Two-Dimensional Nuclear Magnetic Resonance
Authors: Boelens, R. / Scheek, R.M. / Van Boom, J.H. / Kaptein, R.
#9: Journal: Isr.J.Chem. / Year: 1986
Title: Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data: A Lac Repressor Headpiece Structure Based on Information on J-Coupling and from Presence and Absence of Noes
Authors: De Vlieg, J. / Boelens, R. / Scheek, R.M. / Kaptein, R. / Van Gunsteren, W.F.
History
DepositionMar 25, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
B: DNA (5'-D(*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*G)-3')
C: DNA (5'-D(*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
A: Lac Repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4234
Polymers12,4003
Non-polymers231
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

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


Mass: 3413.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#2: DNA chain DNA (5'-D(*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')


Mass: 3293.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#3: Protein Lac Repressor


Mass: 5693.446 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BMH 74-12 / Keywords: POLYPEPTIDE / References: UniProt: P03023
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE AVERAGE PAIRWISE RMSD BETWEEN THE FOUR STRUCTURES (EXCLUDING WATER AND IONS) IS 0.9 ANGSTROMS ON BACKBONE ATOMS (EXCLUDING FIRST AND LAST THREE PROTEIN RESIDUES, AND THE FIRST AND LAST BASE ...Text: THE AVERAGE PAIRWISE RMSD BETWEEN THE FOUR STRUCTURES (EXCLUDING WATER AND IONS) IS 0.9 ANGSTROMS ON BACKBONE ATOMS (EXCLUDING FIRST AND LAST THREE PROTEIN RESIDUES, AND THE FIRST AND LAST BASE PAIR) AND 1.4 ANGSTROMS ON ALL ATOMS. THE DATA SETS INCLUDE THOSE WATERS AND IONS FOR WHICH THE DISTANCES TO THE NEAREST NEIGHBOR ATOM IN PROTEIN AS WELL AS IN DNA DO NOT EXCEED 4 ANGSTROMS.

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR softwareName: GROMOS / Classification: refinement
NMR ensembleConformers submitted total number: 1
NMR ensemble rmsAtom type: all atoms / Distance rms dev: 1.4 Å

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