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- PDB-3i9y: Crystal structure of the V. parahaemolyticus histidine kinase sen... -

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Basic information

Entry
Database: PDB / ID: 3i9y
TitleCrystal structure of the V. parahaemolyticus histidine kinase sensor TorS sensor domain
ComponentsSensor protein
KeywordsTRANSFERASE / stacked two four-helix bundles / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Transmembrane / Two-component regulatory system
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / identical protein binding / plasma membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #920 / Signal transduction histidine kinase, TMAO sensor TorS / Sensor histidine kinase TorS, sensor domain / TorS, sensor domain superfamily / Sensor protein TorS, sensor domain / TorS N-terminal sensor domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #920 / Signal transduction histidine kinase, TMAO sensor TorS / Sensor histidine kinase TorS, sensor domain / TorS, sensor domain superfamily / Sensor protein TorS, sensor domain / TorS N-terminal sensor domain / 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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / 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 speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.16 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


Theoretical massNumber of molelcules
Total (without water)31,5731
Polymers31,5731
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.880, 149.880, 42.712
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Sensor protein


Mass: 31572.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: K-12 / Gene: torS, VPA0675 / Plasmid: pETDuetT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87ID1, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 4.39 Å3/Da / Density % sol: 71.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7-13% PEG 4000, 0.1M Tris pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.98950,0.97940,0.97912,0.96863
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2005 / Details: mirrors
RadiationMonochromator: system consisting of a horizontally deflecting and focusing crystal
Protocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98951
20.97941
30.979121
40.968631
ReflectionResolution: 2.16→20 Å / Num. obs: 29951 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.095 / Χ2: 1.088 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.16-2.235.30.41929440.96599.9
2.23-2.325.50.35329640.951100
2.32-2.425.60.26829671.004100
2.42-2.555.60.21829891.037100
2.55-2.715.60.18629521.069100
2.71-2.925.60.1429921.097100
2.92-3.215.60.129981.133100
3.21-3.675.50.06830011.158100
3.67-4.615.30.0530251.23699.9
4.61-205.10.04531191.23299.7

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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 wavelength110.97915.69-8.51
4 wavelength120.97943.95-11.81
4 wavelength130.96863.84-3.25
4 wavelength140.98951.4-3.69
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.6310.2560.9910.583
2Se600.8280.3190.6090.514
3Se41.3340.5460.1740.0040.334
4Se43.980.5260.1620.5820.285
5Se600.5520.070.3420.302
6Se600.5710.1870.0110.484
7Se10.5260.1780.9760.088
8Se10.5190.4140.050.017
9Se600.5740.4040.0480.288
10Se10.5860.2130.0110.049

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.11phasing
CNS1.2refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.16→19.8 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 1777269 / 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
Rfree0.261 1505 5 %RANDOM
Rwork0.222 ---
obs-29936 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.553 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 74.28 Å2 / Biso mean: 31.671 Å2 / Biso min: 11.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.71 Å20 Å2
3----1.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.16→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 0 72 1927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.056
X-RAY DIFFRACTIONc_angle_deg3.7
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d2.47
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.16→2.28 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 224 4.8 %
Rwork0.239 4452 -
all-4676 -
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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