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- PDB-3i9w: Crystal structure of the E. coli histidine kinase sensor TorS sen... -

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Basic information

Entry
Database: PDB / ID: 3i9w
TitleCrystal structure of the E. coli histidine kinase sensor TorS sensor domain
ComponentsSensor protein torS
KeywordsTRANSFERASE / stacked two four-helix bundles / ATP-binding / Cell inner membrane / Cell membrane / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Transmembrane / Two-component regulatory system
Function / homology
Function and homology information


anaerobic respiration / cellular response to organic substance / histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / phosphorelay signal transduction system / protein dephosphorylation / protein autophosphorylation / membrane => GO:0016020 / ATP binding ...anaerobic respiration / cellular response to organic substance / histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / phosphorelay signal transduction system / protein dephosphorylation / protein autophosphorylation / membrane => GO:0016020 / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #920 / Sensor histidine kinase TorS, sensor domain / TorS, sensor domain superfamily / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #920 / Sensor histidine kinase TorS, sensor domain / TorS, sensor domain superfamily / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) 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 / 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 / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsMoore, J.O. / Hendrickson, W.A.
CitationJournal: Structure / Year: 2009
Title: Structural analysis of sensor domains from the TMAO-responsive histidine kinase receptor TorS
Authors: Moore, J.O. / Hendrickson, W.A.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein torS


Theoretical massNumber of molelcules
Total (without water)32,4491
Polymers32,4491
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.528, 137.112, 123.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sensor protein torS /


Mass: 32449.150 Da / Num. of mol.: 1 / Fragment: UNP residues 35 to 320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b0993, JW5135, torS, yccI / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39453, histidine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 4 Å3/Da / Density % sol: 69.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1-4 butanediol, NaAcetate pH 5.5, NH4SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.99117, 0.97943, 0.97912, 0.96806
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2005 / Details: mirrors
RadiationMonochromator: Kohzu double crystal monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.991171
20.979431
30.979121
40.968061
ReflectionResolution: 2.7→20 Å / Num. obs: 14294 / % possible obs: 97.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.074 / Χ2: 1.296 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.84.30.38313341.06593.2
2.8-2.914.30.25113501.05395.3
2.91-3.044.40.19113631.06596.6
3.04-3.24.40.14314061.11997.4
3.2-3.44.60.11514051.11896.9
3.4-3.666.60.14513951.16998.7
3.66-4.038.30.11714371.60198.9
4.03-4.69.10.07914501.61699.3
4.6-5.779.50.06914731.34299.3
5.77-209.40.04515301.17199.5

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
4
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
4 wavelength110.97915.56-7.97
4 wavelength120.97944.67-11.75
4 wavelength130.96813.65-3.32
4 wavelength140.99121.12-3.34
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se53.8090.1260.1580.2020.607
2Se600.1020.280.1190.633
3Se600.550.4140.0620.646
4Se10.2610.2580.0940.109
5Se10.3260.1110.0330.094
6Se59.680.680.4720.0670.259
7Se19.1910.7980.3830.0450.137

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.08phasing
CNS1.2refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.7→19.68 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 1878859 / 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
Rfree0.302 719 5 %RANDOM
Rwork0.247 ---
obs-14143 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.45 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 139.12 Å2 / Biso mean: 73.572 Å2 / Biso min: 37.09 Å2
Baniso -1Baniso -2Baniso -3
1-21.24 Å20 Å20 Å2
2---32.56 Å20 Å2
3---11.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 0 43 2167
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d17.1
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 117 5.2 %
Rwork0.35 2139 -
all-2256 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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