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- PDB-9epn: Crystal structure of HprS histidine kinase cytoplasmic fragment f... -

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Basic information

Entry
Database: PDB / ID: 9epn
TitleCrystal structure of HprS histidine kinase cytoplasmic fragment from Escherichia coli
ComponentsSensor histidine kinase HprS
KeywordsTRANSFERASE / Histidine kinase / bacterial two-component system
Function / homology
Function and homology information


response to hypochlorite / transferase activity, transferring phosphorus-containing groups / response to copper ion / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / protein kinase activity / DNA damage response / ATP binding / plasma membrane
Similarity search - Function
Heavy metal sensor kinase / : / 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 ...Heavy metal sensor kinase / : / 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. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / GLYCOCHOLIC ACID / IMIDAZOLE / Sensor histidine kinase HprS
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKoczurowska, A. / Bujacz, G. / Pietrzyk-Brzezinska, A.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Arch.Biochem.Biophys. / Year: 2024
Title: Structural and biophysical characterization of the cytoplasmic domains of HprS kinase and its interactions with the cognate regulator HprR.
Authors: Koczurowska, A. / Carrillo, D.R. / Alai, M.G. / Zaklos-Szyda, M. / Bujacz, G. / Pietrzyk-Brzezinska, A.J.
History
DepositionMar 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor histidine kinase HprS
B: Sensor histidine kinase HprS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,08822
Polymers63,1862
Non-polymers2,90220
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint-40 kcal/mol
Surface area26640 Å2
Unit cell
Length a, b, c (Å)64.890, 92.510, 118.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sensor histidine kinase HprS / Hydrogen peroxide response sensor


Mass: 31593.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first two residues (MA) are the remainings from the His-Tag
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: hprS, yedV, b1968, JW1951 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P76339, histidine kinase

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Non-polymers , 6 types, 340 molecules

#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GCH / GLYCOCHOLIC ACID / N-CHOLYLGLYCINE


Mass: 465.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H43NO6
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 90 mM sodium nitrate, 90 mM sodium phosphate dibasic, 90 mM ammonium sulfate, 1.2% CHAPS, 1.2% CHAPSO, 1.2% sodium glycocholate, 1.2% taurocholic acid, 40 mM imidazole pH 6.5, 60 mM MES pH 6. ...Details: 90 mM sodium nitrate, 90 mM sodium phosphate dibasic, 90 mM ammonium sulfate, 1.2% CHAPS, 1.2% CHAPSO, 1.2% sodium glycocholate, 1.2% taurocholic acid, 40 mM imidazole pH 6.5, 60 mM MES pH 6.5, 20% ethylene glycol, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.976264 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976264 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 78650 / % possible obs: 99.7 % / Redundancy: 13.4 % / CC1/2: 0.998 / Net I/σ(I): 18.26
Reflection shellResolution: 1.7→1.8 Å / Mean I/σ(I) obs: 1.16 / Num. unique obs: 163275 / CC1/2: 0.73 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.42 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2173 2099 2.67 %
Rwork0.1891 --
obs0.1898 78595 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4331 0 0 320 4651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084452
X-RAY DIFFRACTIONf_angle_d1.0376026
X-RAY DIFFRACTIONf_dihedral_angle_d17.6082694
X-RAY DIFFRACTIONf_chiral_restr0.063698
X-RAY DIFFRACTIONf_plane_restr0.007759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.34681350.3394917X-RAY DIFFRACTION97
1.74-1.780.27961380.30625019X-RAY DIFFRACTION100
1.78-1.830.34011380.30775057X-RAY DIFFRACTION100
1.83-1.890.27611390.25655058X-RAY DIFFRACTION100
1.89-1.950.24761400.22515084X-RAY DIFFRACTION100
1.95-2.020.25511390.20725067X-RAY DIFFRACTION100
2.02-2.10.24041390.20185080X-RAY DIFFRACTION100
2.1-2.190.22351380.20645003X-RAY DIFFRACTION99
2.19-2.310.24411410.20415128X-RAY DIFFRACTION100
2.31-2.450.25351390.20255088X-RAY DIFFRACTION100
2.45-2.640.21711410.20365128X-RAY DIFFRACTION100
2.64-2.910.23771400.20395117X-RAY DIFFRACTION100
2.91-3.330.20981420.18895157X-RAY DIFFRACTION100
3.33-4.190.20371430.16675219X-RAY DIFFRACTION100
4.19-36.420.1971470.17375374X-RAY DIFFRACTION99
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)
15.19640.4102-0.57015.1015-0.48853.0631-0.52170.4681-0.72-0.70530.701-0.89110.31470.6217-0.14580.9810.04730.19371.02470.08981.134349.296924.184519.1409
24.09410.5992-3.74751.1239-1.469.40410.4594-0.0746-0.03210.1594-0.23410.1662-1.56820.3623-0.18210.63840.08060.05920.50270.02710.613132.902321.80634.4379
34.40040.47570.50163.669-0.55052.08820.4409-0.9805-0.44430.4053-0.14240.163-0.2221-0.089-0.22530.3511-0.0002-0.03840.51110.04120.477314.216111.372551.8387
43.3919-0.38910.24773.54231.16564.9811-0.10590.0817-0.20390.15740.0740.61010.2768-1.00040.0080.3714-0.05390.06390.53070.04380.51920.940832.079640.6273
51.74370.24080.05381.06510.15974.8948-0.0621-0.02740.18610.09150.0676-0.00050.01590.053-0.00530.3790.05530.02220.3304-0.00950.374413.663937.960542.6868
66.16411.1171.62055.81141.51272.1729-0.4140.7768-0.1291-0.59530.26020.55491.1566-0.90750.2490.5095-0.11420.02730.58480.02980.4258.396137.403525.116
71.12540.44431.21754.70070.16022.67660.06220.08240.0085-1.8301-0.5106-0.95820.33171.31120.27521.41110.10890.38421.73910.0080.987847.299118.61465.5786
84.40362.1753-2.44982.689-1.29623.6915-0.22041.073-0.7715-0.84630.1282-0.69360.175-0.1716-0.06640.6360.06050.11250.5869-0.06360.638331.695611.874829.2225
92.52371.6834-0.29381.53290.35980.37920.1244-0.8675-1.58190.30730.089-0.37050.2690.1039-0.1960.4819-0.0167-0.09730.87590.22860.828112.1435-0.289454.4145
104.8062-0.68092.30721.89080.92222.7762-0.2926-0.29111.0519-0.1187-0.16620.4364-1.228-0.10160.34390.59140.0019-0.0760.425-0.01310.549638.52914.322946.1392
112.39220.4820.33122.14441.02494.08590.0751-0.2514-0.21860.2572-0.0944-0.03610.3080.02070.01260.3851-0.02270.00780.34730.00280.378646.8914-5.358652.0959
122.5143-1.4567-0.34594.56680.93673.7430.04220.2322-0.3446-0.1496-0.18410.36170.0547-0.35730.11020.3173-0.022-0.00490.3115-0.03770.341741.4419-2.335639.8508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 176:217)
2X-RAY DIFFRACTION2(chain A and resid 218:248)
3X-RAY DIFFRACTION3(chain A and resid 249:304)
4X-RAY DIFFRACTION4(chain A and resid 305:372)
5X-RAY DIFFRACTION5(chain A and resid 373:445)
6X-RAY DIFFRACTION6(chain A and resid 446:452)
7X-RAY DIFFRACTION7(chain B and resid 204:217)
8X-RAY DIFFRACTION8(chain B and resid 218:254)
9X-RAY DIFFRACTION9(chain B and resid 255:287)
10X-RAY DIFFRACTION10(chain B and resid 288:306)
11X-RAY DIFFRACTION11(chain B and resid 307:390)
12X-RAY DIFFRACTION12(chain B and resid 391:452)

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