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- PDB-1lbh: INTACT LACTOSE OPERON REPRESSOR WITH GRATUITOUS INDUCER IPTG -

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Basic information

Entry
Database: PDB / ID: 1lbh
TitleINTACT LACTOSE OPERON REPRESSOR WITH GRATUITOUS INDUCER IPTG
ComponentsINTACT LACTOSE OPERON REPRESSOR WITH GRATUITOUS INDUCER IPTG
KeywordsTRANSCRIPTION REGULATION / DNA-BINDING / REPRESSOR
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 / Response regulator / Periplasmic binding protein-like I ...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 / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-methylethyl 1-thio-beta-D-galactopyranoside / Lactose operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3.2 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
DepositionFeb 17, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
A: INTACT LACTOSE OPERON REPRESSOR WITH GRATUITOUS INDUCER IPTG
B: INTACT LACTOSE OPERON REPRESSOR WITH GRATUITOUS INDUCER IPTG
C: INTACT LACTOSE OPERON REPRESSOR WITH GRATUITOUS INDUCER IPTG
D: INTACT LACTOSE OPERON REPRESSOR WITH GRATUITOUS INDUCER IPTG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,5818
Polymers154,6284
Non-polymers9534
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13560 Å2
ΔGint-63 kcal/mol
Surface area41700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.200, 75.100, 149.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein
INTACT LACTOSE OPERON REPRESSOR WITH GRATUITOUS INDUCER IPTG


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: LAC I / Plasmid: PIQ / Gene (production host): LAC I / Production host: Escherichia coli (E. coli) / References: UniProt: P03023
#2: Sugar
ChemComp-IPT / 1-methylethyl 1-thio-beta-D-galactopyranoside / ISOPROPYL-1-BETA-D-THIOGALACTOSIDE / 1-(ISOPROPYLTHIO)-BETA-GALACTOPYRANSIDE / 1-methylethyl 1-thio-beta-D-galactoside / 1-methylethyl 1-thio-D-galactoside / 1-methylethyl 1-thio-galactoside


Type: D-saccharide / Mass: 238.301 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H18O5S
IdentifierTypeProgram
isopropyl-1-b-D-thiogalactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.9 %
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

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 18, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 26094 / % possible obs: 97 % / Rmerge(I) obs: 0.091
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 15 Å / Num. measured all: 110526

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 3.2→15 Å / Rfactor Rwork: 0.23 / Rfactor obs: 0.23 / σ(F): 0
Displacement parametersBiso mean: 22 Å2
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8876 0 60 0 8936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.9
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 / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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