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- PDB-9jfj: Crystal structure of the cytoplasmic domain of ZraS in ADP-bound form -

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Basic information

Entry
Database: PDB / ID: 9jfj
TitleCrystal structure of the cytoplasmic domain of ZraS in ADP-bound form
ComponentsSensor histidine kinase ZraS
KeywordsTRANSFERASE / ZraS / Cytoplasmic domain / Sensor histidine kinase / Two-component system / Escherichia coli
Function / homology
Function and homology information


cellular response to lead ion / protein histidine kinase activity / cellular response to zinc ion / cellular response to cell envelope stress / histidine kinase / phosphorelay sensor kinase activity / signal transduction / ATP binding / membrane / plasma membrane
Similarity search - Function
Periplasmic sensor-like domain superfamily / 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/HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Periplasmic sensor-like domain superfamily / 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/HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Sensor histidine kinase ZraS
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsMahapatra, N. / Pandey, S. / Mahanta, P. / Acharya, R.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: Proteins / Year: 2025
Title: Insights Into the Conformational Dynamics of the Cytoplasmic Domain of Metal-Sensing Sensor Histidine Kinase ZraS.
Authors: Mahapatra, N. / Mahanta, P. / Pandey, S. / Acharya, R.
History
DepositionSep 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 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 ZraS
B: Sensor histidine kinase ZraS
C: Sensor histidine kinase ZraS
D: Sensor histidine kinase ZraS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,06212
Polymers105,2564
Non-polymers1,8068
Water00
1
A: Sensor histidine kinase ZraS
B: Sensor histidine kinase ZraS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5316
Polymers52,6282
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-73 kcal/mol
Surface area21820 Å2
MethodPISA
2
C: Sensor histidine kinase ZraS
D: Sensor histidine kinase ZraS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5316
Polymers52,6282
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-72 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.870, 121.790, 88.430
Angle α, β, γ (deg.)90.000, 126.044, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Sensor histidine kinase ZraS


Mass: 26313.912 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: zraS, hydH, b4003, JW3967 / Plasmid: pNIC28Bsa4 / Production host: Escherichia (bacteria) / Strain (production host): LEMO21(DE3) / References: UniProt: P14377, histidine kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: Bipyramidal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Ammonium sulfate, 0.1M Tris pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.49→46.36 Å / Num. obs: 38311 / % possible obs: 99.9 % / Redundancy: 5.96 % / Biso Wilson estimate: 65.86 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1637 / Net I/σ(I): 5.57
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 4.53 % / Rmerge(I) obs: 0.6929 / Mean I/σ(I) obs: 0.72 / Num. unique obs: 4257 / CC1/2: 0.727 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→46.36 Å / SU ML: 0.453 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.9739
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2819 1903 5.01 %
Rwork0.2609 36064 -
obs0.262 37967 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.65 Å2
Refinement stepCycle: LAST / Resolution: 2.49→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6722 0 112 0 6834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01046930
X-RAY DIFFRACTIONf_angle_d1.49259464
X-RAY DIFFRACTIONf_chiral_restr0.09011169
X-RAY DIFFRACTIONf_plane_restr0.00751210
X-RAY DIFFRACTIONf_dihedral_angle_d22.30422415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.550.53551360.47392469X-RAY DIFFRACTION95.63
2.55-2.620.42881200.45742492X-RAY DIFFRACTION96.31
2.62-2.70.44311420.41232558X-RAY DIFFRACTION98.86
2.7-2.790.4161330.38982589X-RAY DIFFRACTION99.38
2.79-2.880.42361340.37082559X-RAY DIFFRACTION99.3
2.89-30.3841460.35782557X-RAY DIFFRACTION99.52
3-3.140.36161270.35792624X-RAY DIFFRACTION99.53
3.14-3.30.33831450.30452574X-RAY DIFFRACTION99.89
3.3-3.510.32781270.28312609X-RAY DIFFRACTION99.89
3.51-3.780.28221300.27642590X-RAY DIFFRACTION99.67
3.78-4.160.28961370.24872586X-RAY DIFFRACTION99.27
4.16-4.760.23631610.21452571X-RAY DIFFRACTION99.56
4.76-60.25311280.23662629X-RAY DIFFRACTION99.78
6-46.360.20031370.19042657X-RAY DIFFRACTION99.71
Refinement TLS params.Method: refined / Origin x: 25.6769210862 Å / Origin y: 24.2169522852 Å / Origin z: 15.9474007049 Å
111213212223313233
T1.22162636433 Å2-0.00410333445813 Å20.200890060104 Å2-0.530190060248 Å2-0.00200838501503 Å2--0.548561910003 Å2
L0.725711900935 °20.782307838925 °2-0.0983464367148 °2-0.62980320839 °2-0.0429406540415 °2--0.0328494853828 °2
S0.158711470126 Å °-0.114058561453 Å °0.0513779495146 Å °0.294215052882 Å °-0.0960175963249 Å °-0.0304537964912 Å °-0.0812407651725 Å °0.037905930508 Å °-0.0616372657524 Å °
Refinement TLS groupSelection details: all

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