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- PDB-9dt3: Crystal structure of the engineered sulfonylurea repressor EsR (L... -

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Basic information

Entry
Database: PDB / ID: 9dt3
TitleCrystal structure of the engineered sulfonylurea repressor EsR (L11-C6), bound to ethametsulfuron-methyl
ComponentsSulfonylurea repressor EsR (L11-C6)
KeywordsDNA BINDING PROTEIN / repressor / transcription / TetR
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 / metal ion binding
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
Chem-RXF / Tetracycline repressor protein class B from transposon Tn10
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 (L11-C6)
B: Sulfonylurea repressor EsR (L11-C6)
C: Sulfonylurea repressor EsR (L11-C6)
D: Sulfonylurea repressor EsR (L11-C6)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3398
Polymers92,6984
Non-polymers1,6424
Water23413
1
A: Sulfonylurea repressor EsR (L11-C6)
B: Sulfonylurea repressor EsR (L11-C6)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1704
Polymers46,3492
Non-polymers8212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-44 kcal/mol
Surface area19430 Å2
MethodPISA
2
C: Sulfonylurea repressor EsR (L11-C6)
D: Sulfonylurea repressor EsR (L11-C6)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1704
Polymers46,3492
Non-polymers8212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-46 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.819, 71.022, 90.526
Angle α, β, γ (deg.)90.000, 92.185, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Sulfonylurea repressor EsR (L11-C6) / Tetracycline repressor protein class B from transposon Tn10


Mass: 23174.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tetR / Production host: Escherichia coli (E. coli) / References: UniProt: P04483
#2: Chemical
ChemComp-RXF / methyl 2-[[4-ethoxy-6-(methylamino)-1,3,5-triazin-2-yl]carbamoylsulfamoyl]benzoate / Ethametsulfuron methyl


Mass: 410.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H18N6O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Magnesium chloride 0.1 M HEPES pH 7.5 30% v/v Polyethylene glycol monomethyl ether 550

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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: MAR CCD 165 mm / 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: 2.8→29.842 Å / Num. obs: 20657 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rsym value: 0.105 / Net I/σ(I): 7.9
Reflection shellResolution: 2.8→2.872 Å / Num. unique obs: 1435 / Rsym value: 0.462

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.842 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.288 / WRfactor Rwork: 0.192 / SU B: 18.409 / SU ML: 0.347 / Average fsc free: 0.9403 / Average fsc work: 0.9754 / Cross valid method: FREE R-VALUE / ESU R Free: 0.445
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2777 1073 5.194 %
Rwork0.1901 19584 -
all0.195 --
obs-20657 99.418 %
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: 61.986 Å2
Baniso -1Baniso -2Baniso -3
1--2.937 Å20 Å2-0.655 Å2
2--4.861 Å2-0 Å2
3----1.868 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 112 13 6169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126251
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166048
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.8738445
X-RAY DIFFRACTIONr_angle_other_deg0.6031.7713828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2255764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.498535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.103101132
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.9910288
X-RAY DIFFRACTIONr_chiral_restr0.0840.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027333
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021375
X-RAY DIFFRACTIONr_nbd_refined0.2420.21455
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.25126
X-RAY DIFFRACTIONr_nbtor_refined0.1860.23037
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23435
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.288
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.217
X-RAY DIFFRACTIONr_nbd_other0.1750.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.24
X-RAY DIFFRACTIONr_mcbond_it5.0935.9173074
X-RAY DIFFRACTIONr_mcbond_other5.0935.9173074
X-RAY DIFFRACTIONr_mcangle_it7.55310.6323832
X-RAY DIFFRACTIONr_mcangle_other7.55210.6333833
X-RAY DIFFRACTIONr_scbond_it6.0946.5813177
X-RAY DIFFRACTIONr_scbond_other6.0936.5813178
X-RAY DIFFRACTIONr_scangle_it9.45911.8544613
X-RAY DIFFRACTIONr_scangle_other9.45811.8544614
X-RAY DIFFRACTIONr_lrange_it11.45358.8917004
X-RAY DIFFRACTIONr_lrange_other11.45358.8917005
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
2.8-2.8720.516770.36914350.37615240.9050.95499.21260.375
2.872-2.950.426760.33213950.33714750.9020.9699.72880.339
2.95-3.0350.502820.28313410.29514300.8950.96599.51050.291
3.035-3.1270.388630.26213540.26914240.9320.96699.50840.266
3.127-3.2290.353650.2512510.25513240.9410.96699.39580.256
3.229-3.3410.407700.22412320.23413030.8930.97299.92330.225
3.341-3.4650.344760.19911940.20712770.930.97899.45180.198
3.465-3.6040.263640.19911290.20311970.9590.97999.66580.202
3.604-3.7620.292650.211030.20511700.9530.98399.82910.206
3.762-3.9430.216590.17610750.17811350.9760.98699.91190.179
3.943-4.1520.24660.1639960.16710630.9620.98899.90590.168
4.152-4.3990.222530.159790.15410330.9660.98899.90320.156
4.399-4.6950.244420.148850.1449300.9660.98899.67740.141
4.695-5.0610.189390.148630.1429040.9760.98999.77880.142
5.061-5.5280.225420.1497730.1548180.970.98899.63330.152
5.528-6.1540.234370.1837010.1867390.9620.98399.86470.182
6.154-7.0560.304280.2086480.2126760.9630.9791000.209
7.056-8.5240.21320.1485400.1515750.9690.98799.47830.154
8.524-11.5910.159220.1224380.1244640.9870.98999.13790.123
11.591-29.8420.37150.3422520.3432960.9250.94190.20270.369

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