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- PDB-2pe5: Crystal Structure of the Lac Repressor bound to ONPG in repressed... -

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Basic information

Entry
Database: PDB / ID: 2pe5
TitleCrystal Structure of the Lac Repressor bound to ONPG in repressed state
Components
  • DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3')
  • Lactose operon repressor
KeywordsTRANSCRIPTION/DNA / Lac repressor / allosteric effectors / gene regulation / DNA-binding / Transcription / Transcription regulation / 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
Transcriptional regulator LacI/GalR-like, sensor domain / LacI-type HTH domain signature. / 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 ...Transcriptional regulator LacI/GalR-like, sensor domain / LacI-type HTH domain signature. / 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 / Response regulator / Periplasmic binding protein-like I / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-nitrophenyl beta-D-galactopyranoside / DNA / DNA (> 10) / Lactose operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsDaber, R. / Stayrook, S.E. / Rosenberg, A. / Lewis, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural analysis of lac repressor bound to allosteric effectors
Authors: Daber, R. / Stayrook, S. / Rosenberg, A. / Lewis, M.
History
DepositionApr 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3')
E: DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3')
F: DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3')
A: Lactose operon repressor
B: Lactose operon repressor
C: Lactose operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,5349
Polymers124,6306
Non-polymers9043
Water00
1
D: DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3')
E: DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3')
A: Lactose operon repressor
B: Lactose operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6896
Polymers83,0874
Non-polymers6022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-58.9 kcal/mol
Surface area30520 Å2
MethodPISA
2
F: DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3')
C: Lactose operon repressor
hetero molecules

F: DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3')
C: Lactose operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6896
Polymers83,0874
Non-polymers6022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area11450 Å2
ΔGint-56.5 kcal/mol
Surface area31460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)253.080, 253.080, 203.247
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: DNA chain DNA (5'-D(*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DT)-3')


Mass: 6132.991 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Lactose operon repressor


Mass: 35410.438 Da / Num. of mol.: 3 / Fragment: sequence database residues 2-331 / Mutation: S61L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lacI / Plasmid: HTUA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P03023
#3: Sugar ChemComp-145 / 2-nitrophenyl beta-D-galactopyranoside / 1-O-[O-NITROPHENYL]-BETA-D-GALACTOPYRANOSE / 2-nitrophenyl beta-D-galactoside / 2-nitrophenyl D-galactoside / 2-nitrophenyl galactoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H15NO8
IdentifierTypeProgram
1-O-[O-nitrophenyl]-b-D-galactopyranoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.03 Å3/Da / Density % sol: 75.52 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.8 M Ammonium Sulfate, 0.1 M Hepes pH 7.5. 11% PEG 400, 14% glycerol, 10X ONPG, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium Sulfate11
2Ammonium Sulfate12
3Hepes11
4Hepes12
5PEG 40011
6PEG 40012
7glycerol11
8glycerol12
9ONPG11
10ONPG12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 19, 2006 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. all: 31342 / Num. obs: 29717 / % possible obs: 99.89 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.176 / Rsym value: 0.176 / Net I/σ(I): 7.3
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 4.37 / Num. unique all: 2090 / Rsym value: 0.504 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EFA

1efa


Resolution: 3.5→19.98 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.82 / SU B: 24.027 / SU ML: 0.398 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.548 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28656 1581 5.1 %RANDOM
Rwork0.23347 ---
all0.23616 29717 --
obs0.23616 29717 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.844 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 3.5→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7418 1046 63 0 8527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228797
X-RAY DIFFRACTIONr_angle_refined_deg1.6272.13712196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965983
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86724.804306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.917151292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2011548
X-RAY DIFFRACTIONr_chiral_restr0.1450.21499
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026133
X-RAY DIFFRACTIONr_nbd_refined0.2240.24303
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2308
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.212
X-RAY DIFFRACTIONr_mcbond_it0.5511.55015
X-RAY DIFFRACTIONr_mcangle_it0.98327890
X-RAY DIFFRACTIONr_scbond_it0.92734559
X-RAY DIFFRACTIONr_scangle_it1.7524.54306
LS refinement shellResolution: 3.5→3.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 107 -
Rwork0.263 2090 -
obs-2090 99.64 %

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