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- PDB-3cgz: Crystal Structure of Salmonella Sensor Kinase PhoQ catalytic domain -

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Basic information

Entry
Database: PDB / ID: 3cgz
TitleCrystal Structure of Salmonella Sensor Kinase PhoQ catalytic domain
ComponentsVirulence sensor histidine kinase phoQ
KeywordsTRANSFERASE / Alpha-Beta Sandwich / Bergerat Fold / ATP-binding / Growth regulation / Inner membrane / Kinase / Magnesium / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Transmembrane / Two-component regulatory system / Virulence
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / regulation of growth / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / membrane => GO:0016020 / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
PhoQ Sensor / PhoQ Sensor superfamily / PhoQ Sensor / HAMP domain profile. / HAMP domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain ...PhoQ Sensor / PhoQ Sensor superfamily / PhoQ Sensor / HAMP domain profile. / HAMP domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Virulence sensor histidine kinase PhoQ / Virulence sensor histidine kinase PhoQ
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsGuarnieri, M.T. / Zhang, L. / Shen, J. / Zhao, R.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The Hsp90 inhibitor radicicol interacts with the ATP-binding pocket of bacterial sensor kinase PhoQ.
Authors: Guarnieri, M.T. / Zhang, L. / Shen, J. / Zhao, R.
History
DepositionMar 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Virulence sensor histidine kinase phoQ
B: Virulence sensor histidine kinase phoQ
C: Virulence sensor histidine kinase phoQ


Theoretical massNumber of molelcules
Total (without water)52,0883
Polymers52,0883
Non-polymers00
Water1,802100
1
A: Virulence sensor histidine kinase phoQ


Theoretical massNumber of molelcules
Total (without water)17,3631
Polymers17,3631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Virulence sensor histidine kinase phoQ


Theoretical massNumber of molelcules
Total (without water)17,3631
Polymers17,3631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Virulence sensor histidine kinase phoQ


Theoretical massNumber of molelcules
Total (without water)17,3631
Polymers17,3631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.121, 64.287, 85.945
Angle α, β, γ (deg.)90.00, 119.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Virulence sensor histidine kinase phoQ


Mass: 17362.570 Da / Num. of mol.: 3 / Fragment: Catalytic Domain, UNP residues 332-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: phoQ / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): XA90
References: UniProt: P14147, UniProt: P0DM80*PLUS, histidine kinase
#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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 27.5% PEG 4000, 0.1MOPS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Sep 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→49.25 Å / Num. all: 33076 / Num. obs: 33043 / % possible obs: 99.9 % / Redundancy: 3.72 % / Rmerge(I) obs: 0.066 / Χ2: 0.99 / Net I/σ(I): 8.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.67 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3284 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
d*TREKdata reduction
MOLREPphasing
RefinementStarting model: PDB entry 1id0

1id0


Resolution: 1.9→30 Å / FOM work R set: 0.803 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3177 -random
Rwork0.234 ---
all-33054 --
obs-31698 95.9 %-
Displacement parametersBiso mean: 41.804 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 0 100 3275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007713
X-RAY DIFFRACTIONc_angle_d1.44382
LS refinement shellResolution: 1.9→1.91 Å /
RfactorNum. reflection
Rfree0.396 52
Rwork0.372 -
obs-519

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