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- PDB-3o1i: Crystal Structure of the TorS sensor domain - TorT complex in the... -

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Basic information

Entry
Database: PDB / ID: 3o1i
TitleCrystal Structure of the TorS sensor domain - TorT complex in the absence of ligand
Components
  • Periplasmic protein TorT
  • Sensor protein TorS
KeywordsSIGNALING PROTEIN / Ligand free / Two component sensor / Periplasmic binding protein / TMAO
Function / homology
Function and homology information


cellular hyperosmotic response / histidine kinase / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / identical protein binding / plasma membrane
Similarity search - Function
TMAO reductase system, periplasmic protein TorT / Signal transduction histidine kinase, TMAO sensor TorS / Sensor protein TorS, sensor domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #920 / Sensor histidine kinase TorS, sensor domain / TorS, sensor domain superfamily / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. ...TMAO reductase system, periplasmic protein TorT / Signal transduction histidine kinase, TMAO sensor TorS / Sensor protein TorS, sensor domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #920 / Sensor histidine kinase TorS, sensor domain / TorS, sensor domain superfamily / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Periplasmic binding protein-like I / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Phosphorelay protein LuxU / Periplasmic protein TorT
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMoore, J.O. / Hendrickson, W.A.
CitationJournal: Structure / Year: 2012
Title: An asymmetry-to-symmetry switch in signal transmission by the histidine kinase receptor for TMAO.
Authors: Moore, J.O. / Hendrickson, W.A.
History
DepositionJul 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Mar 27, 2013Group: Other
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor protein TorS
B: Sensor protein TorS
D: Periplasmic protein TorT
C: Periplasmic protein TorT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5335
Polymers131,1784
Non-polymers3541
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.710, 364.520, 80.810
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 Sensor protein TorS


Mass: 31701.875 Da / Num. of mol.: 2 / Fragment: Sensor Domain (UNP residues 51-323)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: EB10 / Gene: TorS, VPA0675 / Plasmid: pRSFDuet-t / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q87ID1, histidine kinase
#2: Protein Periplasmic protein TorT


Mass: 33887.172 Da / Num. of mol.: 2 / Fragment: UNP residues 31-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: EB10 / Gene: TorT, VPA0674 / Plasmid: pETDuet-t / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB DE3 pLysS / References: UniProt: Q87ID2
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.25 Å3/Da / Density % sol: 62.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1-4% PEG 400, 1.0-1.7M AmSO4, 100mM Tris pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.98009 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2007 / Details: slits and mirrors
RadiationMonochromator: horizontally deflecting and focusing crystal preceded by a vertically focusing mirror.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98009 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 42656 / Num. obs: 42602 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.141 / Rsym value: 0.128 / Net I/σ(I): 11.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.455 / Rsym value: 0.421 / % possible all: 9.8

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Isopropanol bound structure

Resolution: 2.8→19.93 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2050435.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.291 2107 5 %RANDOM
Rwork0.248 ---
obs0.248 42485 99.8 %-
all-42677 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.941 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 65.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.55 Å20 Å2
3----1.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9017 0 21 98 9136
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.62.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 365 5.3 %
Rwork0.343 6583 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3Peg40014C.paramPeg40014C.top

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