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- PDB-8biy: Citrate-free extracytoplasmic PAS domain mutant R93A of sensor hi... -

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Basic information

Entry
Database: PDB / ID: 8biy
TitleCitrate-free extracytoplasmic PAS domain mutant R93A of sensor histidine kinase CitA from Geobacillus thermodenitrificans
ComponentsHistidine kinase
KeywordsSIGNALING PROTEIN / signal transduction / Geobacillus thermodenitrificans / sensor histidine kinase / CitA / sensor domain / extracytoplasmic PAS domain / R93A mutation / two-component signaling system
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / nucleotide binding / plasma membrane
Similarity search - Function
SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / Periplasmic sensor-like domain superfamily / PAS domain / Histidine kinase/HSP90-like ATPase / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain ...SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Single cache domain 3 / Single cache domain 3 / Signal transduction histidine kinase, sporulation regulator SpoOB / Periplasmic sensor-like domain superfamily / PAS domain / Histidine kinase/HSP90-like ATPase / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsBecker, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2025
Title: Mechanism of sensor kinase CitA transmembrane signaling.
Authors: Zhang, X.C. / Xue, K. / Salvi, M. / Schomburg, B. / Mehrens, J. / Giller, K. / Stopp, M. / Weisenburger, S. / Boning, D. / Sandoghdar, V. / Unden, G. / Becker, S. / Andreas, L.B. / Griesinger, C.
History
DepositionNov 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine kinase
B: Histidine kinase
C: Histidine kinase
D: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,51813
Polymers56,1604
Non-polymers1,3589
Water3,981221
1
A: Histidine kinase
C: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0248
Polymers28,0802
Non-polymers9446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1362
Polymers14,0401
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3573
Polymers14,0401
Non-polymers3172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.137, 120.053, 152.137
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Histidine kinase


Mass: 14040.037 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: R93A mutant
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Gene: dctS_2, GTHT12_01458 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W6VSR4, histidine kinase
#2: Chemical
ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.6
Details: 0.2M lithium sulfate, 0.9M sodium di-hydrogen phosphate, 0.6M di-potassium hydrogen phosphate, 0.1M N-cyclohexyl-3-aminopropanesulfonic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→47.12 Å / Num. obs: 70580 / % possible obs: 99.1 % / Redundancy: 12.94 % / Biso Wilson estimate: 27.74 Å2 / Rrim(I) all: 0.049 / Net I/σ(I): 16.33
Reflection shellResolution: 1.61→1.64 Å / Num. unique obs: 2137 / Rrim(I) all: 0.63

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XPREPdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BGB

8bgb


Resolution: 1.61→47.12 Å / SU ML: 0.1865 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.4588
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.223 3585 5.08 %
Rwork0.1913 66995 -
obs0.1929 70580 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.36 Å2
Refinement stepCycle: LAST / Resolution: 1.61→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 83 221 4024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00674166
X-RAY DIFFRACTIONf_angle_d0.97455654
X-RAY DIFFRACTIONf_chiral_restr0.0624638
X-RAY DIFFRACTIONf_plane_restr0.0097747
X-RAY DIFFRACTIONf_dihedral_angle_d9.3289649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.630.31831350.29322442X-RAY DIFFRACTION94.02
1.63-1.660.29641310.24672482X-RAY DIFFRACTION97.83
1.66-1.680.25841400.23782554X-RAY DIFFRACTION98.21
1.68-1.70.26541420.23132488X-RAY DIFFRACTION98.43
1.7-1.730.28331230.22982581X-RAY DIFFRACTION98.72
1.73-1.760.25051320.22722539X-RAY DIFFRACTION98.78
1.76-1.790.23311250.23932548X-RAY DIFFRACTION98.82
1.79-1.820.28521430.23572555X-RAY DIFFRACTION98.9
1.82-1.860.3281490.26672524X-RAY DIFFRACTION99.29
1.86-1.90.33021360.26012555X-RAY DIFFRACTION99.04
1.9-1.940.23741240.21792587X-RAY DIFFRACTION98.76
1.94-1.980.25481260.20642574X-RAY DIFFRACTION99.56
1.98-2.030.22161250.19512581X-RAY DIFFRACTION99.19
2.03-2.090.24011410.20142567X-RAY DIFFRACTION99.41
2.09-2.150.23551350.20432568X-RAY DIFFRACTION99.3
2.15-2.220.25211640.20522558X-RAY DIFFRACTION99.74
2.22-2.30.24141340.20532565X-RAY DIFFRACTION99.63
2.3-2.390.17771280.19222618X-RAY DIFFRACTION99.64
2.39-2.50.2331420.20822607X-RAY DIFFRACTION99.75
2.5-2.630.21291340.19882569X-RAY DIFFRACTION99.67
2.63-2.790.22621470.19052611X-RAY DIFFRACTION99.86
2.79-3.010.23811630.20092610X-RAY DIFFRACTION99.86
3.01-3.310.22451340.19042618X-RAY DIFFRACTION99.96
3.31-3.790.20141330.17472648X-RAY DIFFRACTION100
3.79-4.770.18991570.14942662X-RAY DIFFRACTION100
4.78-47.120.21431420.18472784X-RAY DIFFRACTION99.9

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