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- PDB-6lgq: The crystal complex structure of histidine kinase and response re... -

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Basic information

Entry
Database: PDB / ID: 6lgq
TitleThe crystal complex structure of histidine kinase and response regulator
Components
  • DNA-binding response regulator
  • Histidine kinase KdpD
KeywordsSIGNALING PROTEIN / Two-component system / histidine kinase / response regulator
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / cellular response to potassium ion / phosphorelay response regulator activity / DNA-binding transcription activator activity / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / outer membrane-bounded periplasmic space ...transferase activity, transferring phosphorus-containing groups / cellular response to potassium ion / phosphorelay response regulator activity / DNA-binding transcription activator activity / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / outer membrane-bounded periplasmic space / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / signal transduction / protein homodimerization activity / DNA binding / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / Signal transduction histidine kinase, osmosensitive K+ channel sensor, N-terminal / Sensor protein KdpD, transmembrane domain / KdpD, transmembrane domain superfamily / Osmosensitive K+ channel His kinase sensor domain / Domain of unknown function (DUF4118) / GAF domain / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. ...: / Signal transduction histidine kinase, osmosensitive K+ channel sensor, N-terminal / Sensor protein KdpD, transmembrane domain / KdpD, transmembrane domain superfamily / Osmosensitive K+ channel His kinase sensor domain / Domain of unknown function (DUF4118) / GAF domain / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Histidine kinase/HSP90-like ATPase / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / Histidine kinase-like ATPase, C-terminal domain / cheY-homologous receiver domain / Heat Shock Protein 90 / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / GAF domain / GAF-like domain superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA-binding response regulator / histidine kinase / Sensor protein KdpD / KDP operon transcriptional regulatory protein KdpE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMing, Q.X.
CitationJournal: To Be Published
Title: The crystal complex structure of histidine kinase and response regulator
Authors: Ming, Q.X.
History
DepositionDec 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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

Downloads & links

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Assembly

Deposited unit
C: Histidine kinase KdpD
D: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)54,5282
Polymers54,5282
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-15 kcal/mol
Surface area21640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.799, 63.068, 85.278
Angle α, β, γ (deg.)90.000, 102.528, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Histidine kinase KdpD / Sensor protein KdpD / Two-component sensor histidine kinase / Two-component sensor kinase / Two- ...Sensor protein KdpD / Two-component sensor histidine kinase / Two-component sensor kinase / Two-component system sensor histidine kinase KdbD


Mass: 27321.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: kdbD, kdpD, AKG99_04800, AML35_19290, B9M99_01250, BK383_18195, C5P44_02760, CIJ94_01275, D2188_15845, D9H70_02790, D9J60_00745, DTL90_04085, DU321_01600, EC382_20775, EIA21_11550, EO241_08335, ...Gene: kdbD, kdpD, AKG99_04800, AML35_19290, B9M99_01250, BK383_18195, C5P44_02760, CIJ94_01275, D2188_15845, D9H70_02790, D9J60_00745, DTL90_04085, DU321_01600, EC382_20775, EIA21_11550, EO241_08335, EXX06_11290, EXX23_12490, EXX53_15910, EXX55_10750, EXX87_15770, FNJ83_05465, HMPREF3040_04620, NCTC9119_03628, SAMEA3472056_00110
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A069C8B3, UniProt: P21865*PLUS, histidine kinase
#2: Protein DNA-binding response regulator / KDP operon transcriptional regulatory protein KdpE / Response regulator in two-component regulatory ...KDP operon transcriptional regulatory protein KdpE / Response regulator in two-component regulatory system with KdpD / Transcriptional regulator / Two-component regulatory system response regulator KdpE / Two-component response regulator / Two-component system response regulator / Two-component system response regulator KdpE / VanR-G_1_AY271782


Mass: 27206.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: kdpE_1, kdpE, A8M42_04350, ACU57_12825, AM464_20745, AUQ13_21380, B9T59_04520, BANRA_01744, BANRA_03868, BEN53_05945, BK248_02745, BK334_19180, BON75_19570, BON86_22395, BvCmsHHP001_00776, ...Gene: kdpE_1, kdpE, A8M42_04350, ACU57_12825, AM464_20745, AUQ13_21380, B9T59_04520, BANRA_01744, BANRA_03868, BEN53_05945, BK248_02745, BK334_19180, BON75_19570, BON86_22395, BvCmsHHP001_00776, BvCmsHHP019_01442, BvCmsKSP026_01795, BvCmsSINP011_01149, BW690_07930, C4J69_07925, C4M78_23895, C5N07_14640, C6B13_12830, C9200_17795, CA593_25685, CDL37_26920, CI694_20635, CQP61_19525, CSB64_10560, D2183_02080, D2185_15895, D3821_21875, D3O91_17430, D9D20_12870, DAH34_18930, DB359_02985, DBQ99_18030, DM129_15030, DNQ41_07435, DNX30_24225, DTM25_00915, DWB25_17365, E2119_26455, E2134_18575, EAI52_22440, EC3234A_8c00210, EC3426_01519, ECONIH1_03925, ECTO6_03354, EIA08_00640, EJH97_16770, EL75_3094, EL79_3187, EL80_5454, ELT20_10810, ELT49_12200, ELT58_16530, EPS71_20965, EPS91_08680, EPT01_08635, ExPECSC022_01393, ExPECSC038_02992, EXX71_13740, EYD11_16000, FTV90_11805, FV293_12605, FV295_01400, MS6198_07470, NCTC10766_06081, NCTC13462_01629, NCTC13846_03346, NCTC7922_06598, NCTC7927_03942, NCTC7928_05334, NCTC8450_01686, NCTC9007_02376, NCTC9045_04052, NCTC9062_04757, NCTC9117_04356, NCTC9706_00828, NCTC9777_03550, RK56_025185, SAMEA3472033_02545, SAMEA3472047_02080, SAMEA3472080_00274, SAMEA3484427_03082, SAMEA3484429_03300, SAMEA3752559_01043, SAMEA3753300_04142, SK85_00691
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A061KF22, UniProt: P21866*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 49.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.0, 5% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 10464 / % possible obs: 92.21 % / Redundancy: 3.9 % / Biso Wilson estimate: 49.56 Å2 / Rpim(I) all: 0.026 / Net I/σ(I): 28.84
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 455 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KNY

4kny


Resolution: 3→38.83 Å / SU ML: 0.3651 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.4876
RfactorNum. reflection% reflection
Rfree0.2317 979 10 %
Rwork0.1832 --
obs0.1881 9794 92.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.06 Å2
Refinement stepCycle: LAST / Resolution: 3→38.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3443 0 0 7 3450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523503
X-RAY DIFFRACTIONf_angle_d0.87064751
X-RAY DIFFRACTIONf_chiral_restr0.0508551
X-RAY DIFFRACTIONf_plane_restr0.0057624
X-RAY DIFFRACTIONf_dihedral_angle_d9.41732125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.3655930.2162838X-RAY DIFFRACTION61.57
3.16-3.360.25691390.18651249X-RAY DIFFRACTION93.53
3.36-3.620.22881470.15531324X-RAY DIFFRACTION98.07
3.62-3.980.22371500.17811347X-RAY DIFFRACTION98.23
3.98-4.550.21191470.16971326X-RAY DIFFRACTION97.23
4.55-5.730.24041510.19951357X-RAY DIFFRACTION99.34
5.73-38.830.21031520.19021374X-RAY DIFFRACTION97.32

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