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- PDB-3o1j: Crystal Structure of the TorS sensor domain - TorT complex in the... -

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Basic information

Entry
Database: PDB / ID: 3o1j
TitleCrystal Structure of the TorS sensor domain - TorT complex in the absence of isopropanol
Components
  • Periplasmic protein TorT
  • Sensor protein TorS
KeywordsSIGNALING PROTEIN / Isopropanol bound / 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
ISOPROPYL ALCOHOL / Phosphorelay protein LuxU / Periplasmic protein TorT
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.95 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)131,2986
Polymers131,1784
Non-polymers1202
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.390, 127.669, 306.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sensor protein TorS


Mass: 31701.875 Da / Num. of mol.: 2 / Fragment: Sensor Domain (UNP residues 51-322)
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-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 5.85 Å3/Da / Density % sol: 78.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4-7% isopropanol, 0.9-1.4M NH4Citrate pH 6.5, 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: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.95→25 Å / Num. all: 64446 / Num. obs: 63235 / % possible obs: 98.2 % / Redundancy: 4.1 % / Biso Wilson estimate: -0.2 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.105 / Net I/σ(I): 6.6
Reflection shellResolution: 2.06→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.472 / Num. unique all: 6391 / Rsym value: 0.496 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.95→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1941877.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3263 5.1 %RANDOM
Rwork0.226 ---
all-65714 --
obs-64373 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.7994 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 56 Å2
Baniso -1Baniso -2Baniso -3
1--3.9 Å20 Å20 Å2
2--13.03 Å20 Å2
3----9.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.95→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9070 0 8 41 9119
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.95→3.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 527 5 %
Rwork0.361 10028 -
obs-10028 97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3isoprop.paramisoprop.top

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