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- PDB-6rh1: Revisiting pH-gated conformational switch. Complex HK853-RR468 D5... -

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Basic information

Entry
Database: PDB / ID: 6rh1
TitleRevisiting pH-gated conformational switch. Complex HK853-RR468 D53A pH 7
Components
  • Response regulator
  • Sensor histidine kinase
KeywordsSIGNALING PROTEIN / Histidine Kinase / Response Regulator / Phosphotransfer / Phosphatase
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / phosphorelay response regulator activity / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / DNA binding / ATP binding / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / : / 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. ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / : / 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 / cheY-homologous receiver domain / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Response regulator / histidine kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMideros-Mora, C. / Casino, P. / Marina, A.
Funding support Spain, Ecuador, United Kingdom, 5items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78571-P Spain
Spanish Ministry of Economy and CompetitivenessBFU2016-78606-P Spain
Other government2015-AR2Q9228-01Ecuador
Synchrotron Light Research Instituteu2017072262 Spain
Synchrotron Light Research Institutemx14739 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Revisiting the pH-gated conformational switch on the activities of HisKA-family histidine kinases.
Authors: Mideros-Mora, C. / Miguel-Romero, L. / Felipe-Ruiz, A. / Casino, P. / Marina, A.
History
DepositionApr 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor histidine kinase
B: Sensor histidine kinase
C: Response regulator
D: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,18016
Polymers86,3654
Non-polymers1,81512
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12010 Å2
ΔGint-225 kcal/mol
Surface area29510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.367, 91.146, 176.145
Angle α, β, γ (deg.)90.00, 93.60, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Sensor histidine kinase


Mass: 29378.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0853 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZV7
#2: Protein Response regulator


Mass: 13804.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0468 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYT9
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1,8 M NH4SO4, citrato pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2→87.9 Å / Num. obs: 71301 / % possible obs: 98 % / Redundancy: 5.7 % / CC1/2: 0.998 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.04 Å / Num. unique obs: 4543

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3DGE

3dge


Resolution: 2→87.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.552 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 3563 5 %RANDOM
Rwork0.21154 ---
obs0.21377 67733 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.632 Å2
Baniso -1Baniso -2Baniso -3
1--2.99 Å20 Å20.35 Å2
2--3.02 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2→87.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5524 0 104 348 5976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195713
X-RAY DIFFRACTIONr_bond_other_d0.0020.025439
X-RAY DIFFRACTIONr_angle_refined_deg1.58127747
X-RAY DIFFRACTIONr_angle_other_deg0.966312594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0975703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03624.917240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.939151025
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1811530
X-RAY DIFFRACTIONr_chiral_restr0.0840.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021073
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3454.7662825
X-RAY DIFFRACTIONr_mcbond_other3.3444.7652824
X-RAY DIFFRACTIONr_mcangle_it4.7967.1283523
X-RAY DIFFRACTIONr_mcangle_other4.7957.1293524
X-RAY DIFFRACTIONr_scbond_it4.3145.3352888
X-RAY DIFFRACTIONr_scbond_other4.2485.2992849
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7077.7394165
X-RAY DIFFRACTIONr_long_range_B_refined8.79456.4536191
X-RAY DIFFRACTIONr_long_range_B_other8.76656.1616122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 265 -
Rwork0.335 4952 -
obs--96.88 %

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