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

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Basic information

Entry
Database: PDB / ID: 6swj
TitleThe kinase domain of GanS, a histidine kinase from Geobacillus stearothermophilus (with Pt)
ComponentsHistidine kinase
KeywordsSIGNALING PROTEIN / Histidine kinase / Galactan utilization system / Geobacillus stearothermophilus / two component sensing 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 / SAD / Resolution: 1.762 Å
AuthorsLansky, S. / Shiradski, M. / Lavid, N. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: The kinase domain of GanS, a histidine kinase from Geobacillus stearothermophilus (with Pt)
Authors: Lansky, S. / Shiradski, 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 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4655
Polymers24,6851
Non-polymers7804
Water2,756153
1
A: Histidine kinase
hetero molecules

A: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,93010
Polymers49,3702
Non-polymers1,5618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area4910 Å2
ΔGint-192 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.830, 80.280, 116.360
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-645-

HOH

21A-746-

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: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pt
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.68 %
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: 1.76→50 Å / Num. obs: 22974 / % possible obs: 99.6 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 24.2
Reflection shellResolution: 1.76→1.87 Å / Rmerge(I) obs: 1.186 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6968

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.762→41.719 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.14
RfactorNum. reflection% reflection
Rfree0.2298 1148 5.01 %
Rwork0.2002 --
obs0.2017 22935 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.5 Å2 / Biso mean: 32.0303 Å2 / Biso min: 7.04 Å2
Refinement stepCycle: final / Resolution: 1.762→41.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 4 153 1799
Biso mean--83.88 39.18 -
Num. residues----205
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7623-1.84250.43311380.3856261598
1.8425-1.93960.29921430.24112711100
1.9396-2.06110.26491410.21482690100
2.0611-2.22030.25461430.20482716100
2.2203-2.44370.22951420.20052710100
2.4437-2.79720.25141440.20122736100
2.7972-3.52390.20881450.1952749100
3.5239-41.7190.1991520.18082860100

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