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- PDB-6rh0: Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 6rh0
TitleRevisiting pH-gated conformational switch. Complex HK853-RR468 pH 5.5
Components
  • Response regulator
  • Sensor histidine kinase
KeywordsSIGNALING PROTEIN / Histidine Kinase / Response Regulator / Phosphotransfer / Phosphatase
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / nucleotide binding / identical protein binding / metal ion binding
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / 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: 2.87 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)88,63920
Polymers86,5834
Non-polymers2,05616
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12390 Å2
ΔGint-256 kcal/mol
Surface area30220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.616, 92.933, 174.337
Angle α, β, γ (deg.)90.00, 93.49, 90.00
Int Tables number5
Space group name H-MI121

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Components

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Protein , 2 types, 4 molecules ABCD

#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: 13913.255 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

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Non-polymers , 4 types, 162 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1,5 M HH4SO4, 0,1M bis-tris 5,5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979178 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979178 Å / Relative weight: 1
ReflectionResolution: 2.87→49.21 Å / Num. obs: 24443 / % possible obs: 97.6 % / Redundancy: 3.8 % / CC1/2: 0.998 / Net I/σ(I): 14.1
Reflection shellResolution: 2.87→3.03 Å / Num. unique obs: 3582

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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→49.21 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.876 / SU B: 33.542 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28727 1279 5.2 %RANDOM
Rwork0.24024 ---
obs0.24271 23163 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.475 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å20 Å20.96 Å2
2--4.19 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.87→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5543 0 116 173 5832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195747
X-RAY DIFFRACTIONr_bond_other_d0.0010.025428
X-RAY DIFFRACTIONr_angle_refined_deg1.0222.0017798
X-RAY DIFFRACTIONr_angle_other_deg0.844312574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6675706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87725.02247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.084151021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9121531
X-RAY DIFFRACTIONr_chiral_restr0.0540.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021076
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_it0.2523.942836
X-RAY DIFFRACTIONr_mcbond_other0.2523.942835
X-RAY DIFFRACTIONr_mcangle_it0.4735.9093538
X-RAY DIFFRACTIONr_mcangle_other0.4735.9093539
X-RAY DIFFRACTIONr_scbond_it0.1494.0382911
X-RAY DIFFRACTIONr_scbond_other0.1433.962864
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.2855.9384189
X-RAY DIFFRACTIONr_long_range_B_refined2.5346.1856069
X-RAY DIFFRACTIONr_long_range_B_other2.38146.1196058
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.87→2.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 109 -
Rwork0.306 1689 -
obs--98.57 %
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)
11.2707-0.83661.40892.5871-3.32855.60720.0386-0.2036-0.3054-0.1726-0.2083-0.21390.5620.40670.16970.11220.08290.02260.14640.10640.187348.0173-41.8269-52.5502
21.5006-0.7634-1.28872.48283.02635.17090.0671-0.2320.367-0.1634-0.19390.168-0.5812-0.40650.12690.11490.0736-0.02290.1503-0.08480.198825.9389-16.243-52.7539
33.70951.8011.45964.31221.8646.7072-0.26240.22640.3148-0.26460.5213-0.6421-0.71260.9298-0.25890.0795-0.10210.02120.1519-0.09160.213657.083-14.9967-65.5684
43.67731.9156-1.64913.2964-1.88396.3402-0.29390.2535-0.386-0.31810.49690.54140.692-0.9381-0.2030.0871-0.1244-0.03390.2010.11580.289317.0247-43.4104-65.6131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A246 - 479
2X-RAY DIFFRACTION2B247 - 481
3X-RAY DIFFRACTION3C2 - 123
4X-RAY DIFFRACTION4D2 - 123

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