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- PDB-1jyf: Structure of the Dimeric Lac Repressor with an 11-residue C-termi... -

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Basic information

Entry
Database: PDB / ID: 1jyf
TitleStructure of the Dimeric Lac Repressor with an 11-residue C-terminal Deletion.
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 / MOLECULAR REPLACEMENT / Resolution: 3 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 1.1Apr 27, 2008Group: 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 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 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)37,5352
Polymers37,4431
Non-polymers921
Water32418
1
A: Lactose Operon Repressor
hetero molecules

A: Lactose Operon Repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0704
Polymers74,8852
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+3/2,y,-z+3/41
Buried area3620 Å2
ΔGint-25 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.700, 91.700, 222.300
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-359-

HOH

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Components

#1: Protein Lactose Operon Repressor


Mass: 37442.715 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DELETION
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.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Sodium Citrate, Sodium Acetate, 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→45.6 Å / Num. obs: 9811 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 4.5
Reflection shellHighest resolution: 3 Å / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.5 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 64464
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Lac repressor dimer

Resolution: 3→19.89 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2855017.57 / Data cutoff high rms absF: 2855017.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1009 10.3 %RANDOM
Rwork0.203 ---
obs-9765 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.301 Å2 / ksol: 0.339368 e/Å3
Displacement parametersBiso mean: 44.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.17 Å20 Å20 Å2
2--5.17 Å20 Å2
3----10.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 6 18 2059
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.922.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 159 10.1 %
Rwork0.313 1415 -
obs--98.3 %
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: 10.3 % / Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.7 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_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
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: 0.339 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.313

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