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- PDB-6a8v: PhoQ sensor domain (D179R mutant): analysis of internal cavity -

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Basic information

Entry
Database: PDB / ID: 6a8v
TitlePhoQ sensor domain (D179R mutant): analysis of internal cavity
ComponentsSensor protein PhoQ
KeywordsSIGNALING PROTEIN / sensor
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
Model detailsSensor protein PhoQ
AuthorsYoshitani, K. / Ishii, E. / Taniguchi, K. / Sugimoto, H. / Shiro, Y. / Mori, H. / Akiyama, Y. / Kato, A. / Utsumi, R. / Eguchi, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP20248012 Japan
Japan Society for the Promotion of ScienceJP16K07681 Japan
Japan Society for the Promotion of ScienceJP17J02501 Japan
CitationJournal: Biosci. Biotechnol. Biochem. / Year: 2019
Title: Identification of an internal cavity in the PhoQ sensor domain for PhoQ activity and SafA-mediated control.
Authors: Yoshitani, K. / Ishii, E. / Taniguchi, K. / Sugimoto, H. / Shiro, Y. / Akiyama, Y. / Kato, A. / Utsumi, R. / Eguchi, Y.
History
DepositionJul 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
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: Sensor protein PhoQ
B: Sensor protein PhoQ


Theoretical massNumber of molelcules
Total (without water)34,4532
Polymers34,4532
Non-polymers00
Water52229
1
A: Sensor protein PhoQ


Theoretical massNumber of molelcules
Total (without water)17,2261
Polymers17,2261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sensor protein PhoQ


Theoretical massNumber of molelcules
Total (without water)17,2261
Polymers17,2261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.035, 63.119, 108.389
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sensor protein PhoQ / Sensor histidine protein kinase/phosphatase PhoQ


Mass: 17226.420 Da / Num. of mol.: 2 / Fragment: sensor domain / Mutation: D179R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: phoQ, b1129, JW1115 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P23837, histidine kinase, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.2
Details: 26% (w/v) PEG 3350, 0.2M ammonium tartrate, 0.1M CHES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2014 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 9523 / % possible obs: 96.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 38.41 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.051 / Rrim(I) all: 0.129 / Χ2: 0.87 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.754.60.4264030.8630.2060.4760.59482.6
2.75-2.84.80.3974120.8760.1880.4420.64889.6
2.8-2.8550.3764380.8840.1770.4180.70289.2
2.85-2.915.10.3354450.9260.1540.3710.64992.3
2.91-2.975.40.3424490.9210.1540.3760.73794.3
2.97-3.045.60.3064680.9340.1380.3370.69696.9
3.04-3.125.60.2574760.9580.1170.2830.76198.6
3.12-3.25.60.2214690.9690.0990.2430.85798.3
3.2-3.35.30.2034810.9680.0940.2250.8697
3.3-3.45.50.1924710.970.0850.2110.91298.9
3.4-3.526.60.194980.9790.0790.2071.204100
3.52-3.666.80.1654760.9880.0690.1791.051100
3.66-3.836.70.1544950.9910.0630.1671.114100
3.83-4.036.70.1414890.990.0580.1531.24699.6
4.03-4.296.70.124870.9910.0480.1291.07599.4
4.29-4.626.30.0984950.9910.0420.1070.98399.6
4.62-5.085.50.0934890.9920.0420.1020.93597
5.08-5.816.90.0965030.9890.0390.1040.819100
5.81-7.326.60.0835270.9930.0340.090.703100
7.32-505.90.0465520.9980.0210.0510.41497.7

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BQ8

3bq8


Resolution: 2.7→44.676 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.23
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 431 5.11 %RANDOM
Rwork0.2042 ---
obs0.2074 8437 86.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.46 Å2 / Biso mean: 42.5302 Å2 / Biso min: 3.15 Å2
Refinement stepCycle: final / Resolution: 2.7→44.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2257 0 0 29 2286
Biso mean---19.74 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072368
X-RAY DIFFRACTIONf_angle_d0.9293231
X-RAY DIFFRACTIONf_chiral_restr0.05368
X-RAY DIFFRACTIONf_plane_restr0.007415
X-RAY DIFFRACTIONf_dihedral_angle_d15.2541458
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7001-2.8230.4552440.283663868258
2.823-2.97180.2894350.251477981468
2.9718-3.15790.3136510.24390895980
3.1579-3.40170.2901490.22321027107690
3.4017-3.74380.2995580.2041139119799
3.7438-4.28520.2447610.18511137119899
4.2852-5.39740.2232620.17241157121998
5.3974-44.6820.2493710.20131221129299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8655-0.2796-1.0190.95040.21031.21460.23960.3580.58530.3210.058-0.1473-0.5807-0.1383-0.06760.28830.05390.00910.24240.08250.385768.998446.844810.7207
22.6364-0.3703-1.18961.1206-0.86041.52970.2967-0.1008-0.17980.24610.3205-0.68350.10480.3510.99090.51410.0285-0.29520.6584-0.28430.646782.222744.227922.5429
31.5960.1501-0.33260.21510.51711.5116-0.1198-0.28580.22190.24960.0803-0.190.54870.1850.04460.31290.0698-0.0010.3397-0.0180.251865.768438.336922.9117
40.81540.2605-0.98990.098-0.37081.4010.1693-0.50230.86540.04210.12810.1004-0.8990.4283-0.29280.67180.01260.26110.4724-0.0110.657552.982154.276930.9582
50.7094-0.226-0.24741.25460.48351.76030.27420.00790.1972-0.0160.1427-0.1298-0.10560.1482-0.26530.18840.0819-0.02610.2104-0.02160.278367.636940.617717.7195
63.45421.50183.21271.03721.72923.27620.16370.41180.5286-0.5307-0.01740.3298-0.60950.00340.06590.50080.0960.07020.21880.11880.620255.54951.838119.7785
75.341-0.80930.68621.47172.01233.42140.464-0.3369-0.08050.01850.2352-0.3587-0.23650.2764-0.6040.3315-0.04390.03010.3518-0.12010.298551.981172.72115.965
80.08710.21790.18010.54870.45880.50580.26140.08420.4858-0.3893-0.1325-0.0855-0.6374-0.2594-0.29581.07580.19110.44610.36070.05760.646645.287188.25973.9884
90.6629-1.5759-0.0484.41860.68510.49330.086-0.00720.2869-0.01280.1928-0.405-0.31760.05360.08950.5178-0.12070.33530.5949-0.02480.35156.938577.26635.7413
100.3590.04560.4021.30710.23550.94810.0848-0.16530.3299-0.14540.22840.0155-0.5428-0.50420.06330.59990.21870.08610.31730.060.249143.520974.59112.8328
111.30630.5251-0.21140.55320.17471.46890.0715-0.2551-0.23790.0412-0.13280.0253-0.0895-0.40940.1080.2652-0.0040.01770.2784-0.01430.215943.041763.35655.1981
121.20210.34240.00771.93940.89051.5401-0.0829-0.1374-0.45440.35480.4373-0.41520.3110.667-0.30740.29650.0491-0.09560.3422-0.00640.399153.623957.35290.9898
130.9858-0.2893-0.35221.50220.32310.39140.0654-0.17540.26840.1335-0.08580.2601-0.4054-0.3102-0.85350.40220.26450.15330.4248-0.05150.199743.924579.546911.8562
141.01470.3756-0.87682.2224-0.66730.8148-0.0214-0.5185-0.41510.46820.0569-0.3240.20480.28260.0120.25390.134-0.10380.45360.21990.425756.665857.63467.2467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 62 )A43 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 83 )A63 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 132 )A84 - 132
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 149 )A133 - 149
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 179 )A150 - 179
6X-RAY DIFFRACTION6chain 'A' and (resid 180 through 187 )A180 - 187
7X-RAY DIFFRACTION7chain 'B' and (resid 45 through 61 )B45 - 61
8X-RAY DIFFRACTION8chain 'B' and (resid 62 through 71 )B62 - 71
9X-RAY DIFFRACTION9chain 'B' and (resid 72 through 83 )B72 - 83
10X-RAY DIFFRACTION10chain 'B' and (resid 84 through 102 )B84 - 102
11X-RAY DIFFRACTION11chain 'B' and (resid 103 through 132 )B103 - 132
12X-RAY DIFFRACTION12chain 'B' and (resid 133 through 164 )B133 - 164
13X-RAY DIFFRACTION13chain 'B' and (resid 165 through 179 )B165 - 179
14X-RAY DIFFRACTION14chain 'B' and (resid 180 through 187 )B180 - 187

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