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- PDB-1lbg: LACTOSE OPERON REPRESSOR BOUND TO 21-BASE PAIR SYMMETRIC OPERATOR... -

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Basic information

Entry
Database: PDB / ID: 1lbg
TitleLACTOSE OPERON REPRESSOR BOUND TO 21-BASE PAIR SYMMETRIC OPERATOR DNA, ALPHA CARBONS ONLY
Components
  • DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
  • PROTEIN (LACTOSE OPERON REPRESSOR)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / DNA-BINDING / REPRESSOR / 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
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 domain superfamily / Periplasmic binding protein-like I
Similarity search - Domain/homology
DNA / DNA (> 10) / Lactose operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 4.8 Å
AuthorsLewis, M. / Chang, G. / Horton, N.C. / Kercher, M.A. / Pace, H.C. / Lu, P.
CitationJournal: Science / Year: 1996
Title: Crystal structure of the lactose operon repressor and its complexes with DNA and inducer.
Authors: Lewis, M. / Chang, G. / Horton, N.C. / Kercher, M.A. / Pace, H.C. / Schumacher, M.A. / Brennan, R.G. / Lu, P.
History
DepositionJan 3, 1996Processing site: NDB
Revision 1.0Feb 17, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
F: DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
G: DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
H: DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
A: PROTEIN (LACTOSE OPERON REPRESSOR)
B: PROTEIN (LACTOSE OPERON REPRESSOR)
C: PROTEIN (LACTOSE OPERON REPRESSOR)
D: PROTEIN (LACTOSE OPERON REPRESSOR)


Theoretical massNumber of molelcules
Total (without water)180,4778
Polymers180,4778
Non-polymers00
Water00
1
E: DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
F: DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
A: PROTEIN (LACTOSE OPERON REPRESSOR)
B: PROTEIN (LACTOSE OPERON REPRESSOR)


Theoretical massNumber of molelcules
Total (without water)90,2384
Polymers90,2384
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
H: DNA (5'-D(*GP*AP*AP*TP*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
C: PROTEIN (LACTOSE OPERON REPRESSOR)
D: PROTEIN (LACTOSE OPERON REPRESSOR)


Theoretical massNumber of molelcules
Total (without water)90,2384
Polymers90,2384
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.300, 224.400, 112.100
Angle α, β, γ (deg.)90.00, 95.70, 90.00
Int Tables number5
Space group name H-MC121

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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*T)-3')


Mass: 6462.196 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
PROTEIN (LACTOSE OPERON REPRESSOR) / Coordinate model: Cα atoms only


Mass: 38657.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: GM1 / Gene: LACI / Plasmid: PIQ / Gene (production host): LACI / Production host: Escherichia coli (E. coli) / References: UniProt: P03023

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.5 %
Crystal
*PLUS
Density % sol: 65.5 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8.5 / Method: macro seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
132 %PEG30001drop
20.05 Mpotassium phosphate1drop
30.075 Msodium potassium tartrate1drop
40.055 mMprotein1drop
50.194 mMDNA1drop
629-31 %PEG30001reservoir
70.05 Mpotassium phosphate1reservoir
80.075 Msodium potassium tartrate1reservoir

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Data collection

DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 11283 / % possible obs: 90 % / Rmerge(I) obs: 0.058
Reflection
*PLUS
Highest resolution: 4.8 Å / Lowest resolution: 15 Å / % possible obs: 90 % / Num. measured all: 43976

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
XDSdata reduction
RefinementResolution: 4.8→15 Å / Rfactor Rwork: 0.26 / Rfactor obs: 0.26 / σ(F): 0
Details: GENERATED SYMMETRY MOLECULES YIELD CLOSE CONTACTS IN CRYSTAL PACKING. THIS IS PARTICULARLY TRUE FOR ATOMS OF LAC RESIDUES 351 AND 350 OF CHAIN D WHICH CONFLICT WITH END BASE G IN CHAIN G. ...Details: GENERATED SYMMETRY MOLECULES YIELD CLOSE CONTACTS IN CRYSTAL PACKING. THIS IS PARTICULARLY TRUE FOR ATOMS OF LAC RESIDUES 351 AND 350 OF CHAIN D WHICH CONFLICT WITH END BASE G IN CHAIN G. THE ELECTRON DENSITY FOR THE ENDS OF THE DNA STRANDS IS WEAK. THE POSITION OF THE END BASE G IN DNA CHAIN G SHOULD BE USED WITH CAUTION.
Displacement parametersBiso mean: 15 Å2
Refinement stepCycle: LAST / Resolution: 4.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 1716 0 0 3144
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 4.8 Å / Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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