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- PDB-1jwl: Structure of the Dimeric lac Repressor/Operator O1/ONPF Complex -

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Basic information

Entry
Database: PDB / ID: 1jwl
TitleStructure of the Dimeric lac Repressor/Operator O1/ONPF Complex
Components
  • 5'-D(*AP*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP*AP*TP*T)-3'
  • 5'-D(*TP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3'
  • Lactose Operon Repressor
KeywordsTRANSCRIPTION/DNA / Lac Repressor / Gene Regulation / DNA-Bending / 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
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 domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily ...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 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-fucopyranoside / DNA / DNA (> 10) / Lactose operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsBell, C.E. / Lewis, M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystallographic analysis of Lac repressor bound to natural operator O1.
Authors: Bell, C.E. / Lewis, M.
History
DepositionSep 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 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
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 5 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 5 CHAIN(S). BIOMOLECULE 1 IS COMPLETE BUT BIOMOLECULE 2 IS INCOMPLETE. BIOMOLECULE 2 DOES NOT CONTAIN THE DNA CHAINS BECAUSE THEY ARE DISORDERED. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: 5'-D(*AP*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP*AP*TP*T)-3'
E: 5'-D(*TP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3'
A: Lactose Operon Repressor
B: Lactose Operon Repressor
C: Lactose Operon Repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2448
Polymers121,3895
Non-polymers8563
Water00
1
D: 5'-D(*AP*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP*AP*TP*T)-3'
E: 5'-D(*TP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3'
A: Lactose Operon Repressor
B: Lactose Operon Repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2026
Polymers85,6324
Non-polymers5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lactose Operon Repressor
hetero molecules

C: Lactose Operon Repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0844
Polymers71,5142
Non-polymers5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Unit cell
Length a, b, c (Å)255.771, 255.771, 206.795
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 5'-D(*AP*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*GP*AP*TP*AP*AP*CP*AP*AP*TP*T)-3'


Mass: 7152.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: O1 top strand
#2: DNA chain 5'-D(*TP*AP*AP*TP*TP*GP*TP*TP*AP*TP*CP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*TP*C)-3'


Mass: 6965.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: O1 bottom strand
#3: Protein Lactose Operon Repressor


Mass: 35756.797 Da / Num. of mol.: 3 / Fragment: C-terminal deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: LacI / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03023
#4: 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.: 3 / 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: 5.36 Å3/Da / Density % sol: 77.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2PEG40011
3HEPES11
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1
21.8 Mammonium sulfate12
38.2 %(w/v)PEG40012
40.1 MHEPES12

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
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: 4→16 Å / Num. all: 68073 / Num. obs: 20847 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.3 % / Biso Wilson estimate: 45 Å2 / Rsym value: 0.111 / Net I/σ(I): 7.9
Reflection shellHighest resolution: 4 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.277 / % possible all: 93.9
Reflection
*PLUS
Num. measured all: 68073 / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
% possible obs: 93.9 % / Rmerge(I) obs: 0.277

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFA

1efa


Resolution: 4→9.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 128004.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1953 9.9 %RANDOM
Rwork0.249 ---
obs0.249 19784 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.8743 Å2 / ksol: 0.361311 e/Å3
Displacement parametersBiso mean: 67.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å212.83 Å20 Å2
2---0.16 Å20 Å2
3---0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 4→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6641 571 60 0 7272
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.54
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it1.372
X-RAY DIFFRACTIONc_scangle_it2.342.5
LS refinement shellResolution: 4→4.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 325 10.1 %
Rwork0.272 2886 -
obs--94.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAM.ONPFTOP.ONPF
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 67.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.54
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: 0.291 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.272

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