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- PDB-2paf: Crystal Structure of the Lactose Repressor bound to anti-inducer ... -

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Basic information

Entry
Database: PDB / ID: 2paf
TitleCrystal Structure of the Lactose Repressor bound to anti-inducer ONPF in induced state
ComponentsLactose operon repressor
KeywordsTRANSCRIPTION / Lac repressor / allosteric effectors / gene 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
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 domain superfamily / Response regulator / Periplasmic binding protein-like I ...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 domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-nitrophenyl beta-D-fucopyranoside / Lactose operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsDaber, R.
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
DepositionMar 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Lactose operon repressor
B: Lactose operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0844
Polymers57,5142
Non-polymers5712
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-22 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.541, 77.541, 212.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Lactose operon repressor


Mass: 28756.938 Da / Num. of mol.: 2
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
#2: Sugar ChemComp-NPF / 2-nitrophenyl beta-D-fucopyranoside / ORTHONITROPHENYL-BETA-D-FUCOPYRANOSIDE / 2-nitrophenyl 6-deoxy-beta-D-galactopyranoside / 2-nitrophenyl beta-D-fucoside / 2-nitrophenyl D-fucoside / 2-nitrophenyl fucoside


Type: D-saccharide / Mass: 285.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO7
IdentifierTypeProgram
orthonitrophenyl-b-D-fucopyranosideIUPAC 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.4 M Sodium Acetate, 0.1 M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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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: Jul 6, 2006 / Details: Osmic Blue Max mirrors
RadiationProtocol: 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: 8745 / Num. obs: 8685 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.166 / Rsym value: 0.166 / Net I/σ(I): 5.9
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 5 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.336 / % possible all: 99.5

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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→19.81 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.871 / SU B: 25.07 / SU ML: 0.402 / Cross valid method: THROUGHOUT / ESU R Free: 0.664 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26516 413 4.8 %RANDOM
Rwork0.19537 ---
obs0.19856 8252 99.09 %-
all-8745 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.204 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 3.5→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4028 0 40 0 4068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224128
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9875616
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1955536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51924.815162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.38215704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7991526
X-RAY DIFFRACTIONr_chiral_restr0.1090.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023028
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.270.22359
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.22854
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9641.52736
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36424302
X-RAY DIFFRACTIONr_scbond_it1.92931462
X-RAY DIFFRACTIONr_scangle_it3.3124.51314
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.584 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 23 -
Rwork0.217 583 -
obs--99.67 %

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