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- PDB-9jpe: the DISMED2 domain of RetS -

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Basic information

Entry
Database: PDB / ID: 9jpe
Titlethe DISMED2 domain of RetS
Componentshistidine kinase
KeywordsMEMBRANE PROTEIN / DISMED2 / MP / Sensor Domain
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane
Similarity search - Function
7TM-DISM receptor, extracellular domain, type 2 / 7TM-DISM receptor, extracellular domain, type 1 / 7TM diverse intracellular signalling / 7TMR-DISM extracellular 2 / 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 ...7TM-DISM receptor, extracellular domain, type 2 / 7TM-DISM receptor, extracellular domain, type 1 / 7TM diverse intracellular signalling / 7TMR-DISM extracellular 2 / 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Noradrenaline / histidine kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsWang, C.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: crystal structure of the DISMED2 domain of RetS at 3.5 Angstrom resolution
Authors: Wang, C.C.
History
DepositionSep 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0742
Polymers17,9031
Non-polymers1701
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.582, 80.582, 51.349
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein histidine kinase / the DISMED2 domain of RetS


Mass: 17903.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: retS, PA4856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HUV7, histidine kinase
#2: Chemical ChemComp-E5E / Noradrenaline


Mass: 170.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12NO3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M BIs-Tris Propane pH 8.5, 0.2 M NaI, 20% peg3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 39591 / % possible obs: 97.12 % / Redundancy: 7.6 % / Biso Wilson estimate: 82.73 Å2 / CC1/2: 0.917 / Net I/σ(I): 2.68
Reflection shellResolution: 3.5→4.4 Å / Mean I/σ(I) obs: 1.11 / Num. unique obs: 19940 / CC1/2: 0.64 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIXdev_5246refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JYB

3jyb


Resolution: 3.5→43.3 Å / SU ML: 0.5261 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3258 230 10.04 %
Rwork0.2714 2060 -
obs0.2762 2290 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.6 Å2
Refinement stepCycle: LAST / Resolution: 3.5→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1149 0 12 0 1161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571196
X-RAY DIFFRACTIONf_angle_d0.94831628
X-RAY DIFFRACTIONf_chiral_restr0.0538169
X-RAY DIFFRACTIONf_plane_restr0.0109211
X-RAY DIFFRACTIONf_dihedral_angle_d13.7447453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-4.40.36841120.3163999X-RAY DIFFRACTION97.71
4.41-43.30.30271180.24581061X-RAY DIFFRACTION96.56
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.56845522794-2.92365943787-0.1111712604247.676938008522.139819076694.22260797951-1.45303650509-0.3627912288780.09873068678111.60170924491.22889050031.0088307435-0.5869005480780.1193049637470.245422584721.38264519593-0.1007735594640.1111647875660.795836572537-0.03807509959070.761944369217-0.602469300381-12.985942285814.0775542163
24.320416407493.681427968041.150792023245.296256450431.986707880622.677550914350.388081582952.855834037931.08443725858-1.86895405099-0.04098367960070.3579604216561.49355075273-0.407927686025-0.1353421920921.044532809240.03119337242810.05377155545170.7458678283490.2813973349940.823272626003-2.4926647182-7.669883451877.15599303801
32.62286796414-1.54802464095-0.847911824941.955967510030.4314935343121.087075075590.4037986131320.5944678808650.343794295567-0.483959995184-0.148840213533-0.4563206816970.364236359842-0.719603158851-0.3230650995880.977859810902-0.0337716167306-0.03133984155830.896450953855-0.2442220795650.7193150490351.89542397307-17.730004283615.9840475316
41.489624492381.55585267332-0.5788719650053.424838281541.48510874918.710549140540.5818657605110.2193246369370.5207338227420.4038136746620.580796501355-0.4357221226581.35783181189-1.16937590634-0.6437866778790.5753667284740.02035115814950.09695018142630.412794467172-0.01007318349830.606664705006-4.0653308904-29.032088143210.9640527652
50.893827487731-0.3163260029381.51990854783.51755952957-0.2812597173422.418591354480.2449664089140.2850456873180.862766964571-0.7379120130470.3379504411741.116914756040.807479452593-0.970704395479-0.308493381390.648217893749-0.03548042422230.08196167557020.8101650431340.01713885425470.80678547084-10.838267773-19.16481127966.13909994453
61.75895803839-1.807070749360.1642414728792.10195914091-0.04084491673010.0493275051808-0.346144133642-0.292156177496-0.3156569272182.222412942140.001386754675380.890266081370.0187021285511-0.480175209210.2849095021270.976050251779-0.1943432038720.01502492441560.8956915353040.07494550627170.820037080508-15.2537278885-29.76098444518.7285684872
71.238003410420.04622814333390.4517423223230.0732448536430.6096879042961.974839733040.1105490913550.322175046521-0.146599270419-0.361186338096-0.185714793545-0.299661828944-0.666735653939-1.29980172105-0.1323385068150.759117537688-0.008111557372060.1249664519710.6491788369320.035565865890.468264520436-4.20367352365-27.099624185911.3720109138
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 48 through 61 )48 - 611 - 14
22chain 'A' and (resid 62 through 71 )62 - 7115 - 24
33chain 'A' and (resid 72 through 95 )72 - 9525 - 48
44chain 'A' and (resid 96 through 112 )96 - 11249 - 65
55chain 'A' and (resid 113 through 130 )113 - 13066 - 83
66chain 'A' and (resid 131 through 145 )131 - 14584 - 98
77chain 'A' and (resid 146 through 185 )146 - 18599 - 138

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