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- PDB-1efa: CRYSTAL STRUCTURE OF THE LAC REPRESSOR DIMER BOUND TO OPERATOR AN... -

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Basic information

Entry
Database: PDB / ID: 1efa
TitleCRYSTAL STRUCTURE OF THE LAC REPRESSOR DIMER BOUND TO OPERATOR AND THE ANTI-INDUCER ONPF
Components
  • DNA (5'-D(*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
  • LAC REPRESSOR
KeywordsTRANSCRIPTION/DNA / protein-dna complex / helix-turn-helix / gene regulation / molecular switch / 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 / SYNCHROTRON / Resolution: 2.6 Å
AuthorsBell, C.E. / Lewis, M.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: A closer view of the conformation of the Lac repressor bound to operator.
Authors: Bell, C.E. / Lewis, M.
#1: Journal: Science / Year: 1996
Title: Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
Authors: Lewis, M. / Chang, G. / Horton, N.C. / Kercher, M.A. / Pace, H.C.
#2: Journal: Science / Year: 1995
Title: Crystal structure of lac repressor core tetramer and its implications for DNA looping
Authors: Friedman, A.M. / Fischmann, T.O. / Steitz, T.A.
#3: Journal: Structure / Year: 1999
Title: The solution structure of lac repressor headpiece 62 complexed to a symmetrical lac operator sequence determined by NMR and restrained molecular dynamics
Authors: Spronk, C.A.E.M. / Bonvin, A.M.J.J. / Radha, P.K. / Melacini, G. / Boelens, R.
#4: Journal: J.Mol.Biol. / Year: 1996
Title: Refined structure of lac repressor headpiece (1-56) determined by relaxation matrix calculations from 2D and 3D NOE data: change of tertiary structure upon binding to the lac operator
Authors: Slijper, M. / Bonvin, A.M. / Boelens, R. / Kaptein, R.
History
DepositionFeb 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 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 2.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: DNA (5'-D(*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
E: DNA (5'-D(*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
A: LAC REPRESSOR
B: LAC REPRESSOR
C: LAC REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0518
Polymers120,1955
Non-polymers8563
Water1,11762
1
D: DNA (5'-D(*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
E: DNA (5'-D(*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')
A: LAC REPRESSOR
B: LAC REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0086
Polymers84,4384
Non-polymers5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: LAC REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0422
Polymers35,7571
Non-polymers2851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)251.438, 251.438, 204.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settingtrigonal
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-907-

HOH

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Components

#1: DNA chain DNA (5'-D(*GP*AP*AP*T*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*AP*AP*TP*T)-3')


Mass: 6462.196 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein LAC REPRESSOR


Mass: 35756.797 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-333 / Mutation: ALA109THR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P03023
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG 400, HEPES, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2ammonium sulfate11
3PEG 40011
4Glycerol11
5ammonium sulfate12
6PEG 40012
7Glycerol12
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlLac dimer1
410 %PEG40012
52.0 Msodium sulphate1
60.1 MHEPES1
714 %glycerol1
2DNA11.5-fold molar excess
3ONPF110-fold excess

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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 / Date: Jan 11, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→17 Å / Num. all: 75989 / Num. obs: 74896 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.5
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.402 / Num. unique all: 6272 / % possible all: 100
Reflection
*PLUS
Num. measured all: 392400
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.6→10 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 953713.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3485 5 %RANDOM
Rwork0.247 ---
obs0.247 69506 93.1 %-
all-75989 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.17 Å2 / ksol: 0.477 e/Å3
Displacement parametersBiso mean: 69.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å27.39 Å20 Å2
2---1.63 Å20 Å2
3---3.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7022 694 60 62 7838
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it0.821.5
X-RAY DIFFRACTIONc_mcangle_it1.482
X-RAY DIFFRACTIONc_scbond_it0.972
X-RAY DIFFRACTIONc_scangle_it1.572.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 510 4.9 %
Rwork0.332 9977 -
obs--84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PADNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION4PARAM.ONPFTOP.ONPF
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

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