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

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Entry
Database: PDB / ID: 1lcd
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 / 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_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_asym_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

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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
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)3 / -
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
#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
#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) / 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.: 49 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR ensembleConformers submitted total number: 3

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