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- PDB-1tlf: UNPRECEDENTED QUATERNARY STRUCTURE OF E. COLI LAC REPRESSOR CORE ... -

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Basic information

Entry
Database: PDB / ID: 1tlf
TitleUNPRECEDENTED QUATERNARY STRUCTURE OF E. COLI LAC REPRESSOR CORE TETRAMER: IMPLICATIONS FOR DNA LOOPING
ComponentsLAC REPRESSOR
KeywordsTRANSCRIPTION REGULATION
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
ETHYL MERCURY ION / 1-methylethyl 1-thio-beta-D-galactopyranoside / Lactose operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsFriedman, A.M. / Fischmann, T.O. / Steitz, T.A.
CitationJournal: Science / Year: 1995
Title: Crystal structure of lac repressor core tetramer and its implications for DNA looping.
Authors: Friedman, A.M. / Fischmann, T.O. / Steitz, T.A.
History
DepositionMar 6, 1995Processing site: BNL
Revision 1.0Jul 31, 1995Provider: 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 / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / 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
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: LAC REPRESSOR
B: LAC REPRESSOR
C: LAC REPRESSOR
D: LAC REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,49112
Polymers128,6194
Non-polymers1,8728
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-95 kcal/mol
Surface area41400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.160, 64.730, 117.940
Angle α, β, γ (deg.)90.00, 91.75, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 284 / 2: CIS PROLINE - PRO B 284 / 3: CIS PROLINE - PRO C 284 / 4: CIS PROLINE - PRO C 332 / 5: CIS PROLINE - PRO D 284

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Components

#1: Protein
LAC REPRESSOR


Mass: 32154.693 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P03023
#2: Chemical
ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5Hg
#3: 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
Nonpolymer detailsTHE MOLECULE WAS CRYSTALLIZED AS A COMPLEX WITH ISOPROPYL-BETA-D-THIOGLACTOPYRANOSIDE AND THE ETHYL ...THE MOLECULE WAS CRYSTALLIZED AS A COMPLEX WITH ISOPROPYL-BETA-D-THIOGLACTOPYRANOSIDE AND THE ETHYL MERCURIC ION, WHICH IS FOUND BOUND TO RESIDUE CYS281. THESE MOIETIES ARE INCLUDED AS HETATM RECORDS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal grow
*PLUS
Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMNaMES11
20.1 mMIPTG11
30.02 %(w/v)11NaN3
417 mg/mlethylmercury phosphate11
5100 mMNaMES12
64 %(w/v)PEG600012
70.1 mMIPTG12
80.02 %(w/v)12NaN3
90.010 mMEDTA11

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Data collection

ReflectionResolution: 2.6→8 Å / Num. obs: 37549 / % possible obs: 97.5 % / Observed criterion σ(I): 2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.222 / Rfactor obs: 0.222 / Highest resolution: 2.6 Å
Details: THE C1 AND HG ATOMS OF THE EMC HET GROUP ARE CHEMICALLY BOUND. THE BOND DISTANCE BETWEEN THEM IS GREATER THAN EXPECTED DUE TO THE LACK OF BONDING RESTRAINT IN THE REFINEMENT AND LIMITED RESOLUTION.
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10712 0 116 0 10828
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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