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- PDB-1lcc: STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BAS... -
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Basic information
Entry | Database: PDB / ID: 1lcc | ||||||
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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 | ||||||
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![]() | GENE REGULATION/DNA / DNA / HALF-OPERATOR / LAC OPERATOR / LAC REPRESSOR / HEADPIECE / GENE REGULATION-DNA COMPLEX | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR | ||||||
![]() | Chuprina, V.P. / Rullmann, J.A.C. / Lamerichs, R.M.J.N. / Van Boom, J.H. / Boelens, R. / Kaptein, R. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() Title: NMR Based Docking Studies of Lac Repressor Headpiece on a Lac Operator Fragment Authors: Rullmann, J.A.C. / Boelens, R. / Kaptein, R. #5: ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 39.8 KB | Display | ![]() |
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PDB format | ![]() | 22.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 299.4 KB | Display | ![]() |
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Full document | ![]() | 299.2 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 3413.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / ![]() |
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#2: DNA chain | Mass: 3293.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / ![]() |
#3: Protein | Mass: 5693.446 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | 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 ...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 software | Name: GROMOS / Classification: refinement |
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NMR ensemble | Conformers submitted total number: 1 |
NMR ensemble rms | Atom type: all atoms / Distance rms dev: 1.4 Å |