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- PDB-9dt2: Crystal structure of the engineered sulfonylurea repressor EsR (L... -

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Basic information

Entry
Database: PDB / ID: 9dt2
TitleCrystal structure of the engineered sulfonylurea repressor EsR (L7-D1), apo form
ComponentsSulfonylurea repressor EsR (L7-D1)
KeywordsDNA BINDING PROTEIN / engineered / ligand / repressor / transcription
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription
Similarity search - Function
Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSchreiter, E.R. / Leija, C. / Kakani, N.K. / McBride, K.E. / Looger, L.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Design and evolution of agrochemical-responsive gene switches for field crops
Authors: McBride, K.E. / Kakani, N.K. / Fang, J. / Leija, C. / Hermanson, F. / Chan, M. / Cho, H.-J. / Richey, C. / Madrigal, A. / Gordon-Kamm, B. / Lowe, K. / Lenderts, B. / Arling, M. / Anand, A. / ...Authors: McBride, K.E. / Kakani, N.K. / Fang, J. / Leija, C. / Hermanson, F. / Chan, M. / Cho, H.-J. / Richey, C. / Madrigal, A. / Gordon-Kamm, B. / Lowe, K. / Lenderts, B. / Arling, M. / Anand, A. / Wang, N. / Hoerster, G. / McGonigle, B. / Liu, Q. / Falco, C.S. / Lassner, M. / Looger, L.L. / Schreiter, E.R. / Marvin, J.S. / Bozhanova, N.G.
History
DepositionSep 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfonylurea repressor EsR (L7-D1)


Theoretical massNumber of molelcules
Total (without water)23,2161
Polymers23,2161
Non-polymers00
Water00
1
A: Sulfonylurea repressor EsR (L7-D1)

A: Sulfonylurea repressor EsR (L7-D1)


Theoretical massNumber of molelcules
Total (without water)46,4312
Polymers46,4312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4010 Å2
ΔGint-52 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.440, 72.440, 95.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Sulfonylurea repressor EsR (L7-D1) / TetR / TetR protein / TetR(B) / Tetracycline repressor protein TetR / Tetracycline resistance ...TetR / TetR protein / TetR(B) / Tetracycline repressor protein TetR / Tetracycline resistance operon repressor protein


Mass: 23215.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: TetR, teTR, tetR(B), CQ842_25520, D3G36_22370, D3G36_27460, D9E49_27735, D9E49_28675, E5H86_28100, E5H86_30860, EHD79_25975, EHD79_28355, EIZ93_26115, FJQ40_26740, FPI65_29665, FPS11_29235, ...Gene: TetR, teTR, tetR(B), CQ842_25520, D3G36_22370, D3G36_27460, D9E49_27735, D9E49_28675, E5H86_28100, E5H86_30860, EHD79_25975, EHD79_28355, EIZ93_26115, FJQ40_26740, FPI65_29665, FPS11_29235, FPS11_30125, GAJ12_26625, GP965_14335, GP975_09140, GP979_15410, GQM21_16135, GRW05_13910, HIE29_003744, HIE29_005530, HL601_26020, HL601_27135, IPF_209
Production host: Escherichia coli (E. coli) / References: UniProt: B1VCF0
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES sodium pH 7.5 2% v/v Polyethylene glycol 400 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→45.147 Å / Num. obs: 4955 / % possible obs: 100 % / Redundancy: 7.5 % / Rsym value: 0.122 / Net I/σ(I): 12.8
Reflection shellResolution: 3.1→3.31 Å / Num. unique obs: 342 / Rsym value: 0.583

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→45.147 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.897 / SU B: 26.253 / SU ML: 0.454 / Cross valid method: FREE R-VALUE / ESU R Free: 0.507
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2976 261 5.267 %
Rwork0.2336 4694 -
all0.237 --
obs-4955 99.899 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 64.023 Å2
Baniso -1Baniso -2Baniso -3
1-3.104 Å20 Å20 Å2
2--3.104 Å2-0 Å2
3----6.208 Å2
Refinement stepCycle: LAST / Resolution: 3.1→45.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 0 0 1365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121383
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161371
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.8471859
X-RAY DIFFRACTIONr_angle_other_deg0.5721.7653153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5475171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.24857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.61910261
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.531061
X-RAY DIFFRACTIONr_chiral_restr0.080.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021593
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02299
X-RAY DIFFRACTIONr_nbd_refined0.2790.2415
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.21315
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2695
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2761
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0350.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1130.236
X-RAY DIFFRACTIONr_nbd_other0.2060.2108
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.22
X-RAY DIFFRACTIONr_mcbond_it5.9396.078696
X-RAY DIFFRACTIONr_mcbond_other5.9396.079696
X-RAY DIFFRACTIONr_mcangle_it9.44210.872863
X-RAY DIFFRACTIONr_mcangle_other9.43910.871864
X-RAY DIFFRACTIONr_scbond_it5.96.765687
X-RAY DIFFRACTIONr_scbond_other5.8966.766688
X-RAY DIFFRACTIONr_scangle_it9.71112.208996
X-RAY DIFFRACTIONr_scangle_other9.70612.206997
X-RAY DIFFRACTIONr_lrange_it13.94763.5111711
X-RAY DIFFRACTIONr_lrange_other13.94363.5131712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.1-3.1810.316180.263420.2633600.9290.9521000.224
3.181-3.2670.495140.2753180.2833320.8480.941000.241
3.267-3.3610.365190.2883100.2933290.9080.931000.25
3.361-3.4640.44140.2583220.2643360.8950.9421000.234
3.464-3.5770.353130.2622950.2673080.9050.9471000.234
3.577-3.7020.319130.2683030.2713160.9420.9441000.24
3.702-3.8410.214110.2332880.2322990.9660.9621000.213
3.841-3.9960.323250.2332660.2392910.9250.9591000.207
3.996-4.1730.334230.2232490.2342720.9420.9611000.19
4.173-4.3740.251100.1922580.1942680.9730.9751000.176
4.374-4.6090.294160.2082400.2152560.9530.9681000.186
4.609-4.8850.305130.1992290.2052420.9210.9731000.183
4.885-5.2180.207160.2162200.2152360.9690.9671000.19
5.218-5.630.26100.1952020.1972120.9580.9731000.169
5.63-6.1570.19790.2691890.2661980.9750.9521000.24
6.157-6.8680.374100.2721730.2781830.9490.9541000.238
6.868-7.90.79480.21650.2141730.7730.9731000.189
7.9-9.6030.17110.1921330.1891450.9750.97799.31030.201
9.603-13.2830.28770.1941130.2011210.9870.97799.17360.208
13.283-45.1470.12310.399790.3988100.88498.76540.412

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