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- PDB-6swk: The kinase domain of GanS, a histidine kinase from Geobacillus st... -

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Basic information

Entry
Database: PDB / ID: 6swk
TitleThe kinase domain of GanS, a histidine kinase from Geobacillus stearothermophilus
ComponentsHistidine kinase
KeywordsSIGNALING PROTEIN / Two component sensing system / Geobacillus stearothermophilus / histidine kinase / galactan utilization system
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, internal region / : / Histidine kinase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases ...Signal transduction histidine kinase, internal region / : / Histidine kinase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Signal transduction histidine kinase-related protein, C-terminal / 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
: / histidine kinase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.742 Å
AuthorsLansky, S. / Shiradsky, M. / Lavid, N. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: The kinase domain of GanS, a histidine kinase from Geobacillus stearothermophilus
Authors: Lansky, S. / Shiradsky, M. / Lavid, N. / Shoham, Y. / Shoham, G.
History
DepositionSep 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine kinase


Theoretical massNumber of molelcules
Total (without water)24,6851
Polymers24,6851
Non-polymers00
Water1,802100
1
A: Histidine kinase

A: Histidine kinase


Theoretical massNumber of molelcules
Total (without water)49,3702
Polymers49,3702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area3790 Å2
ΔGint-27 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.950, 80.160, 116.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-537-

HOH

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Components

#1: Protein Histidine kinase


Mass: 24684.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: GT94_12015 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A087LIA4, UniProt: W8QF84*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 3350, 1.05 M KSCN, 0.1 M Bis-Tris propane pH 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 23784 / % possible obs: 99.1 % / Redundancy: 23.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 20.7
Reflection shellResolution: 1.74→1.85 Å / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3574

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SWJ

6swj


Resolution: 1.742→41.777 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.91
RfactorNum. reflection% reflection
Rfree0.2521 1188 5.01 %
Rwork0.2191 --
obs0.2208 23710 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.28 Å2 / Biso mean: 39.7739 Å2 / Biso min: 16.48 Å2
Refinement stepCycle: final / Resolution: 1.742→41.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 0 100 1729
Biso mean---44.15 -
Num. residues----203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.742-1.82090.43151370.4061259293
1.8209-1.91690.32721460.29752787100
1.9169-2.0370.24221490.23082823100
2.037-2.19420.30281470.23542789100
2.1942-2.4150.29961490.22442826100
2.415-2.76440.31911510.23372861100
2.7644-3.48260.25591510.22422862100
3.4826-41.7770.2031580.19432982100

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