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- PDB-4rzt: Lac repressor engineered to bind sucralose, sucralose-bound tetramer -

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Basic information

Entry
Database: PDB / ID: 4rzt
TitleLac repressor engineered to bind sucralose, sucralose-bound tetramer
ComponentsLac repressor
KeywordsTRANSCRIPTION / sucralose / lacI / lac repressor / lactose operon repressor / protein design / allostery / Escherichia coli
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
sucralose / : / Lactose operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsArbing, M.A. / Cascio, D. / Sawaya, M.R. / Kosuri, S. / Church, G.M.
CitationJournal: Nat.Methods / Year: 2016
Title: Engineering an allosteric transcription factor to respond to new ligands.
Authors: Taylor, N.D. / Garruss, A.S. / Moretti, R. / Chan, S. / Arbing, M.A. / Cascio, D. / Rogers, J.K. / Isaacs, F.J. / Kosuri, S. / Baker, D. / Fields, S. / Church, G.M. / Raman, S.
History
DepositionDec 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lac repressor
B: Lac repressor
C: Lac repressor
D: Lac repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,1248
Polymers163,5344
Non-polymers1,5914
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11370 Å2
ΔGint-99 kcal/mol
Surface area42790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.590, 74.080, 149.160
Angle α, β, γ (deg.)90.00, 119.91, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUARGARGAA62 - 35583 - 376
21LEULEUARGARGBB62 - 35583 - 376
12GLNGLNGLNGLNAA60 - 36081 - 381
22GLNGLNGLNGLNCC60 - 36081 - 381
13LEULEUARGARGAA62 - 35583 - 376
23LEULEUARGARGDD62 - 35583 - 376
14LEULEUARGARGBB62 - 35583 - 376
24LEULEUARGARGCC62 - 35583 - 376
15LEULEULEULEUBB62 - 35683 - 377
25LEULEULEULEUDD62 - 35683 - 377
16LEULEUARGARGCC62 - 35583 - 376
26LEULEUARGARGDD62 - 35583 - 376

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Lac repressor / Transcriptional regulator / LacI family


Mass: 40883.488 Da / Num. of mol.: 4 / Mutation: D149T, V150A, I156L, S193D
Source method: isolated from a genetically manipulated source
Details: N-terminal thrombin-cleavable 6xHis-tag / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 MG1655 / Gene: b0345, ECDH1ME8569_0332, EcDH1_3261, lacI / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: C9QQT3, UniProt: P03023*PLUS
#2: Polysaccharide
4-chloro-4-deoxy-alpha-D-galactopyranose-(1-2)-1,6-dichloro-1,6-dideoxy-beta-D-fructofuranose / sucralose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 397.634 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucralose
DescriptorTypeProgram
[][b-D-Fruf1chloro6chloro]{[(2+1)][a-D-Galp4chloro]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M HEPES, pH7.5, 10% polyethylene glycol 6000, and 5% MPD, pH 7.4, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.03→81.67 Å / Num. obs: 24030 / % possible obs: 84.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.24
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.03-3.180.582.04111.3
3.18-3.270.5512.27134.9
3.27-3.370.5252.36167.6
3.37-3.470.4882.75190.8
3.47-3.580.3873.53198.8
3.58-3.710.294.79198.7
3.71-3.850.2086.51198.6
3.85-4.010.1767.89198.5
4.01-4.190.1369.63196.9
4.19-4.390.10612.86199.3
4.39-4.630.09515.35199.2
4.63-4.910.09316.03198.7
4.91-5.250.08416.33198.6
5.25-5.670.08215.76197.4
5.67-6.210.07917.66199.3
6.21-6.940.06220.72198.3
6.94-8.020.03827.65197.1
8.02-9.820.02934.91198
9.82-13.880.02737.6197.7
13.880.02538.32193.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
PHASERphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→81.66 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.919 / SU B: 59.306 / SU ML: 0.437 / SU R Cruickshank DPI: 0.4767 / Cross valid method: THROUGHOUT / ESU R Free: 0.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24335 1230 5.1 %RANDOM
Rwork0.20513 ---
obs0.20713 22808 85.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.245 Å2
Baniso -1Baniso -2Baniso -3
1--3.53 Å2-0 Å2-1 Å2
2--2.96 Å2-0 Å2
3---1.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.83 Å
Refinement stepCycle: LAST / Resolution: 3.1→81.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8679 0 92 16 8787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198891
X-RAY DIFFRACTIONr_bond_other_d0.0040.028571
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.98812143
X-RAY DIFFRACTIONr_angle_other_deg1.003319591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08951188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97224.799323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.949151412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.141552
X-RAY DIFFRACTIONr_chiral_restr0.0710.21531
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110144
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021856
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0535.074764
X-RAY DIFFRACTIONr_mcbond_other3.0545.074763
X-RAY DIFFRACTIONr_mcangle_it5.027.6045948
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1525.2794127
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A170370.07
12B170370.07
21A181650.04
22C181650.04
31A170480.07
32D170480.07
41B171680.07
42C171680.07
51B175210.04
52D175210.04
61C171870.07
62D171870.07
LS refinement shellResolution: 3.1→3.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 8 -
Rwork0.374 225 -
obs--11.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.61030.38641.30144.918-0.05912.70340.32610.154-0.5672-0.5842-0.449-0.01290.3720.06390.12280.23070.11550.11070.07270.03660.2166-60.619-19.3194185.1021
25.2277-0.08380.11272.86420.16142.29720.16530.92020.8509-0.8765-0.4773-0.0208-0.14790.25410.31210.39240.17320.11580.28940.2410.3519-62.61284.3471175.716
34.5808-0.09081.3984.0851-0.41723.4748-0.0745-0.0850.44810.25-0.14210.2508-0.2778-0.08770.21660.58530.03070.01760.044-0.04510.0847-35.43449.779142.5396
43.46880.10611.40812.61930.32844.64490.3698-0.6374-0.3120.5336-0.1970.53280.6538-0.806-0.17280.7912-0.16650.05170.20540.06050.2363-44.4976-13.8871145.9985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 501
2X-RAY DIFFRACTION2B62 - 501
3X-RAY DIFFRACTION3C60 - 501
4X-RAY DIFFRACTION4D62 - 501

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