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- PDB-3n6u: Effector binding domain of TsaR in complex with its inducer p-tol... -

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Basic information

Entry
Database: PDB / ID: 3n6u
TitleEffector binding domain of TsaR in complex with its inducer p-toluenesulfonate
ComponentsLysR type regulator of tsaMBCD
KeywordsTRANSCRIPTION REGULATOR / Rossmann fold
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PARA-TOLUENE SULFONATE / HTH-type transcriptional regulator TsaR
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsMonferrer, D. / Uson, I.
CitationJournal: To be Published
Title: Structural studies on the effector binding domain of TsaR
Authors: Monferrer, D. / Perillo, M. / Sola, M. / Uson, I.
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LysR type regulator of tsaMBCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1978
Polymers22,3701
Non-polymers8277
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: LysR type regulator of tsaMBCD
hetero molecules

A: LysR type regulator of tsaMBCD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,39316
Polymers44,7392
Non-polymers1,65414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area2630 Å2
ΔGint-23 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)51.500, 95.710, 82.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein LysR type regulator of tsaMBCD


Mass: 22369.703 Da / Num. of mol.: 1 / Fragment: Effector binding domain, UNP residues 91-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Strain: T-2 / Gene: tsa, tsaR / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P94678
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TSU / PARA-TOLUENE SULFONATE / P-Toluenesulfonic acid


Mass: 172.202 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8O3S
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.5M ammonium sulfate, 0.1M sodium acetate pH4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54179 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.87→25.78 Å / Num. obs: 17327 / % possible obs: 99.7 % / Redundancy: 1.88 % / Rmerge(I) obs: 0.0267 / Rsym value: 0.032 / Net I/σ(I): 20.23
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 4.75 / Rsym value: 0.21 / % possible all: 98.3

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Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→25.78 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.686 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26655 879 5.1 %RANDOM
Rwork0.21971 ---
obs0.22195 16430 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.112 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.77 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.87→25.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 51 44 1671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221665
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0821.9982281
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.765204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4322.60969
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94115241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6941514
X-RAY DIFFRACTIONr_chiral_restr0.1340.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0221282
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4031.51038
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.33921669
X-RAY DIFFRACTIONr_scbond_it3.4783627
X-RAY DIFFRACTIONr_scangle_it5.554.5612
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.869→1.917 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 62 -
Rwork0.264 1150 -
obs--97.51 %

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