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- PDB-3bqa: Crystal Structure of an E.coli PhoQ Sensor Domain Mutant -

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Basic information

Entry
Database: PDB / ID: 3bqa
TitleCrystal Structure of an E.coli PhoQ Sensor Domain Mutant
ComponentsSensor protein phoQ
Keywordssignaling protein / transferase / histidine kinase sensor domain / ATP-binding / Inner membrane / Magnesium / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Transmembrane / Two-component regulatory system
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / cellular response to magnesium starvation / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / kinase activity / signal transduction / ATP binding ...osmosensory signaling via phosphorelay pathway / cellular response to magnesium starvation / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / kinase activity / signal transduction / ATP binding / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
PhoQ sensor 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. ...PhoQ sensor 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. / Beta-Lactamase / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsCheung, J. / Hendrickson, W.A. / Waldburger, C.D.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structure of a Functional Dimer of the PhoQ Sensor Domain.
Authors: Cheung, J. / Bingman, C.A. / Reyngold, M. / Hendrickson, W.A. / Waldburger, C.D.
History
DepositionDec 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein phoQ
B: Sensor protein phoQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3393
Polymers34,2432
Non-polymers961
Water6,053336
1
A: Sensor protein phoQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2172
Polymers17,1211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sensor protein phoQ


Theoretical massNumber of molelcules
Total (without water)17,1211
Polymers17,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.417, 44.417, 151.858
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Sensor protein phoQ


Mass: 17121.355 Da / Num. of mol.: 2 / Mutation: E148Q, D149N, D150N, D151N, D152N, E154Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: phoQ / Plasmid: pSC101-derived plasmid / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23837, histidine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growMethod: vapor diffusion
Details: PEG4000, sodium acetate, ammonium sulphate, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 19615 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.035 / Χ2: 1.042 / Net I/σ(I): 22.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.089 / Num. unique all: 1936 / Χ2: 1.044 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.86 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1348977.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 999 5.1 %RANDOM
Rwork0.168 ---
obs-19573 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.358 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 5 336 2827
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it3.411.5
X-RAY DIFFRACTIONc_mcangle_it4.362
X-RAY DIFFRACTIONc_scbond_it5.242
X-RAY DIFFRACTIONc_scangle_it7.12.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 180 5.6 %
Rwork0.182 3054 -
all-3234 -
obs--98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramion.top
X-RAY DIFFRACTION3ion.paramwater.top

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