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- PDB-1jye: Structure of a Dimeric Lac Repressor with C-terminal Deletion and... -

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Basic information

Entry
Database: PDB / ID: 1jye
TitleStructure of a Dimeric Lac Repressor with C-terminal Deletion and K84L Substitution
ComponentsLactose Operon Repressor
KeywordsTRANSCRIPTION / Gene Regulation / Protein Stability / Protein DNA-binding
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
Lactose operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBell, C.E. / Barry, J. / Matthews, K.S. / Lewis, M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structure of a variant of lac repressor with increased thermostability and decreased affinity for operator.
Authors: Bell, C.E. / Barry, J. / Matthews, K.S. / Lewis, M.
History
DepositionSep 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Apr 14, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_site
Item: _pdbx_struct_assembly_prop.biol_id / _struct_site.pdbx_auth_asym_id ..._pdbx_struct_assembly_prop.biol_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactose Operon Repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5192
Polymers37,4271
Non-polymers921
Water4,234235
1
A: Lactose Operon Repressor
hetero molecules

A: Lactose Operon Repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0384
Polymers74,8532
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+3/2,y,-z+3/41
Buried area3610 Å2
ΔGint-23 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.007, 87.007, 224.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-374-

HOH

21A-421-

HOH

31A-450-

HOH

41A-512-

HOH

51A-525-

HOH

61A-526-

HOH

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Components

#1: Protein Lactose Operon Repressor


Mass: 37426.691 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DELETION MUTANT / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: LacI / Plasmid: pJC-1 / Production host: Escherichia coli (E. coli) / Strain (production host): TB-1 / References: UniProt: P03023
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DIFFERENCE AT POSITION 109 IS A DIFFERENCE IN THE SEQUENCE REPORTED BY FARABAUGH, P.J. (1978) ...THE DIFFERENCE AT POSITION 109 IS A DIFFERENCE IN THE SEQUENCE REPORTED BY FARABAUGH, P.J. (1978) NATURE 274, 765-769 AND THE PIQ SEQUENCE REPORTED BY BETZ J.L. (1986) GENE 42, 283-292. THE PROTEIN IN THIS STRUCTURE IS DERIVED FROM PIQ AND HAS THR AT POSITION 109.

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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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Sodium Acetate, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.3-1.5 Msodium acetate1reservoir
20.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: BRANDEIS - B4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→17 Å / Num. obs: 44403 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 5.8 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.5
Reflection shellHighest resolution: 1.7 Å / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 7.2 / % possible all: 72.7
Reflection
*PLUS
Num. measured all: 258845
Reflection shell
*PLUS
% possible obs: 72.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: lac repressor

Resolution: 1.7→9.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1304025.4 / Data cutoff high rms absF: 1304025.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 4366 10 %RANDOM
Rwork0.223 ---
all-43541 --
obs-43541 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.1617 Å2 / ksol: 0.520559 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1-2.71 Å20 Å20 Å2
2--2.71 Å20 Å2
3----5.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.02 Å
Refinement stepCycle: LAST / Resolution: 1.7→9.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 6 235 2267
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 580 10.1 %
Rwork0.284 5181 -
obs--74 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.284 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.284

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