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- PDB-6a8u: PhoQ sensor domain (wild type): analysis of internal cavity -

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Basic information

Entry
Database: PDB / ID: 6a8u
TitlePhoQ sensor domain (wild type): analysis of internal cavity
ComponentsSensor protein PhoQ
KeywordsSIGNALING PROTEIN / sensor protein
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: 1.848 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 ScienceP20248012 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)34,3692
Polymers34,3692
Non-polymers00
Water4,954275
1
A: Sensor protein PhoQ


Theoretical massNumber of molelcules
Total (without water)17,1841
Polymers17,1841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sensor protein PhoQ


Theoretical massNumber of molelcules
Total (without water)17,1841
Polymers17,1841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.030, 68.230, 112.896
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: 17184.314 Da / Num. of mol.: 2 / Fragment: sensor domain
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.: 275 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.2
Details: 32% (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: 1.85→50 Å / Num. obs: 24449 / % possible obs: 94.1 % / Redundancy: 11.3 % / Biso Wilson estimate: 19.56 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.023 / Rrim(I) all: 0.079 / Χ2: 0.949 / Net I/σ(I): 8.5 / Num. measured all: 276450
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.887.80.36312030.9420.1310.3871.00694.3
1.88-1.928.70.33412220.9520.1140.3541.0295.1
1.92-1.9510.10.29312060.9770.0940.3091.03395
1.95-1.9910.60.25711970.9760.080.271.01594.5
1.99-2.0411.20.22911730.9840.070.241.01292.5
2.04-2.0811.10.19411570.9840.0590.2041.00489.6
2.08-2.1411.70.16611080.990.050.1741.01487.2
2.14-2.19120.1512230.9930.0440.1560.97497.1
2.19-2.26120.1512600.9930.0440.1561.00796.6
2.26-2.33120.1312190.9940.0380.1350.96596
2.33-2.4111.70.11512380.9940.0340.120.96595.5
2.41-2.5111.50.10412090.9940.0310.1080.94493.5
2.51-2.6311.90.09411760.9960.0280.0980.94491.1
2.63-2.7612.10.08212650.9970.0240.0850.93297.7
2.76-2.9412.20.07412720.9970.0220.0770.91597.4
2.94-3.1611.90.06412670.9970.0190.0670.91696.6
3.16-3.4811.70.05612210.9980.0170.0580.91693.6
3.48-3.9912.30.0512720.9980.0150.0520.8996.4
3.99-5.0211.80.04612180.9970.0140.0480.83989.9
5.02-5011.50.04213430.9990.0130.0440.76592.4

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Processing

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

3bq8


Resolution: 1.848→43.493 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 1276 5.23 %RANDOM
Rwork0.1692 23128 --
obs0.1721 24404 94.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.06 Å2 / Biso mean: 24.5508 Å2 / Biso min: 6.43 Å2
Refinement stepCycle: final / Resolution: 1.848→43.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2266 0 0 275 2541
Biso mean---30.43 -
Num. residues----280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062437
X-RAY DIFFRACTIONf_angle_d0.7853336
X-RAY DIFFRACTIONf_chiral_restr0.055380
X-RAY DIFFRACTIONf_plane_restr0.005429
X-RAY DIFFRACTIONf_dihedral_angle_d13.1211511
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8482-1.92220.27731590.2172500265994
1.9222-2.00970.22761400.18212546268694
2.0097-2.11560.23331400.1682359249988
2.1156-2.24820.21811450.1622607275297
2.2482-2.42170.25681490.17452567271696
2.4217-2.66540.25011300.1772543267393
2.6654-3.0510.24111290.18132676280597
3.051-3.84360.19641370.16092662279995
3.8436-43.50490.20681470.15542668281592
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)
10.4894-0.0799-0.01250.2206-0.26990.597-0.10260.06660.03410.0896-0.0026-0.0393-0.14150.135-0.01670.0752-0.0026-0.00440.0567-0.00170.066761.580345.894512.535
20.0668-0.01490.12980.02050.00860.39440.01050.30090.61330.0542-0.10350.07990.05030.21180.01470.1641-0.0272-0.01010.21050.03480.327364.994252.688119.0307
31.07020.0029-0.46730.1328-0.17520.96570.0727-0.0985-0.01350.039-0.03880.0073-0.06170.0490.01780.0713-0.0040.00270.07080.00080.088649.524645.109123.4873
40.0502-0.161-0.09510.12810.08350.33870.16620.11210.1399-0.1252-0.1169-0.1031-0.12430.01280.01810.08310.02060.02630.09550.0060.112157.208144.896915.4583
51.08810.26170.26581.15660.56121.0250.27930.18350.03250.2582-0.2538-0.23070.40020.55490.14110.17810.072-0.00030.2448-0.01470.123541.069278.079217.8386
60.1340.01160.11010.08460.02920.1810.07530.2052-0.1212-0.0855-0.1673-0.0996-0.18030.2344-0.02580.23540.09910.02280.27180.0290.258838.162991.41125.8796
7-0.1657-0.386-0.49641.021.07560.5721-0.00820.0192-0.0263-0.0182-0.09160.10520.0242-0.0043-0.01370.160.04260.00170.1384-0.01790.130237.086472.0956.4257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 71 )A43 - 71
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 83 )A72 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 164 )A84 - 164
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 187 )A165 - 187
5X-RAY DIFFRACTION5chain 'B' and (resid 42 through 62 )B42 - 62
6X-RAY DIFFRACTION6chain 'B' and (resid 63 through 83 )B63 - 83
7X-RAY DIFFRACTION7chain 'B' and (resid 84 through 186 )B84 - 186

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