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- PDB-7k1c: TtgR in complex with resveratrol -

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Basic information

Entry
Database: PDB / ID: 7k1c
TitleTtgR in complex with resveratrol
ComponentsHTH-type transcriptional regulator TtgR
KeywordsTRANSCRIPTION / TtgR / TetR family / epistasis / resveratrol
Function / homology
Function and homology information


DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding
Similarity search - Function
Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / 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
RESVERATROL / HTH-type transcriptional regulator TtgR
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBingman, C.A. / Nishikawa, K.K. / Smith, R.W. / Raman, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM07215 United States
Department of Defense (DOD, United States)W911NF-17-1-0043 United States
CitationJournal: Nat Commun / Year: 2021
Title: Epistasis shapes the fitness landscape of an allosteric specificity switch.
Authors: Nishikawa, K.K. / Hoppe, N. / Smith, R. / Bingman, C. / Raman, S.
History
DepositionSep 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator TtgR
B: HTH-type transcriptional regulator TtgR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2866
Polymers47,7812
Non-polymers5054
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-33 kcal/mol
Surface area18540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.730, 64.500, 223.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein HTH-type transcriptional regulator TtgR / Toluene efflux pump ttgABC operon repressor


Mass: 23890.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: DOT-T1E / Gene: ttgR, T1E_0244 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9AIU0
#2: Chemical ChemComp-STL / RESVERATROL


Mass: 228.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 nL of protein at 9.8 mg/mL (0.41 millimolar) in 5mM HEPES pH 7.5, 50 mM NaCl, 0.3 mM TCEP and 0.5 millimolar resveratrol was equilibrated against 250 nL 18% PEG4000, 0.2M MgCl2, 0.1M ...Details: 200 nL of protein at 9.8 mg/mL (0.41 millimolar) in 5mM HEPES pH 7.5, 50 mM NaCl, 0.3 mM TCEP and 0.5 millimolar resveratrol was equilibrated against 250 nL 18% PEG4000, 0.2M MgCl2, 0.1M bistris HCl pH 6.5 in a SD2 plate using a Mosquito crystallization robot. Samples were cryoprotected with reservoir solution supplemented with 35% PEG4000. Samples looped in Mitegen micro mounts were flash cooled by immersion in liquid nitrogen. Crystals were grown at 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2018 / Details: 3.0 Undulator C(111) monochromator
RadiationMonochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→28.63 Å / Num. obs: 33367 / % possible obs: 99.88 % / Redundancy: 14.4 % / Biso Wilson estimate: 36.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07704 / Rpim(I) all: 0.02123 / Rrim(I) all: 0.07997 / Net I/σ(I): 22.92
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 14.9 % / Rmerge(I) obs: 1.294 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 3316 / CC1/2: 0.739 / CC star: 0.922 / Rpim(I) all: 0.3446 / Rrim(I) all: 1.339 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XDN

2xdn


Resolution: 1.9→28.63 Å / SU ML: 0.2689 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.3456
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 2020 6.06 %
Rwork0.1834 31329 -
obs0.1859 33349 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.83 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 36 193 3524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163410
X-RAY DIFFRACTIONf_angle_d1.22544613
X-RAY DIFFRACTIONf_chiral_restr0.0607522
X-RAY DIFFRACTIONf_plane_restr0.0096605
X-RAY DIFFRACTIONf_dihedral_angle_d14.61131278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.40861010.32582243X-RAY DIFFRACTION100
1.95-20.31982020.26142138X-RAY DIFFRACTION99.96
2-2.060.26841010.23372306X-RAY DIFFRACTION99.96
2.06-2.130.23482020.20382092X-RAY DIFFRACTION99.96
2.13-2.20.24781010.19732259X-RAY DIFFRACTION100
2.2-2.290.2461010.19082266X-RAY DIFFRACTION100
2.29-2.390.24382020.18752179X-RAY DIFFRACTION100
2.39-2.520.28241010.1842258X-RAY DIFFRACTION99.96
2.52-2.680.24182020.1912165X-RAY DIFFRACTION100
2.68-2.880.20551010.19032319X-RAY DIFFRACTION100
2.88-3.170.23712020.19862136X-RAY DIFFRACTION100
3.17-3.630.23631010.182333X-RAY DIFFRACTION99.96
3.63-4.570.18631010.15042310X-RAY DIFFRACTION100
4.58-28.630.1942020.17662325X-RAY DIFFRACTION99.18
Refinement TLS params.Method: refined / Origin x: -2.23568965908 Å / Origin y: -1.72437874147 Å / Origin z: -27.5488402525 Å
111213212223313233
T0.314087166873 Å2-0.0275905518016 Å20.00211462179769 Å2-0.23168048064 Å20.0306468746882 Å2--0.331226206033 Å2
L0.928771770845 °20.118160549906 °20.21718404951 °2-0.651514006954 °20.0777807853124 °2--1.79893126554 °2
S-0.0470256162053 Å °0.0216054535373 Å °-0.0123399419704 Å °-0.073283870364 Å °0.103480022803 Å °0.0622534619855 Å °-0.0587542305592 Å °-0.00133198626096 Å °0.000257741395886 Å °
Refinement TLS groupSelection details: all

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