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- PDB-6rgy: Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 6rgy
TitleRevisiting pH-gated conformational switch. Complex HK853-RR468 pH 7.5
Components
  • Osmosensitive K+ channel histidine kinase KdpD
  • Response regulator
KeywordsSIGNALING PROTEIN / Histidine Kinase / Response Regulator / Phosphotransfer / Phosphatase
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor / 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. / Histidine kinase-like ATPase, C-terminal domain / Response regulator receiver domain / cheY-homologous receiver domain / Heat Shock Protein 90 / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / CITRIC ACID / Response regulator / histidine kinase / Osmosensitive K+ channel histidine kinase KdpD
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 ...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 / 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 / _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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Osmosensitive K+ channel histidine kinase KdpD
B: Osmosensitive K+ channel histidine kinase KdpD
C: Response regulator
D: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,92722
Polymers86,5834
Non-polymers2,34418
Water5,441302
1
A: Osmosensitive K+ channel histidine kinase KdpD
C: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,31910
Polymers43,2922
Non-polymers1,0288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-125 kcal/mol
Surface area17500 Å2
MethodPISA
2
B: Osmosensitive K+ channel histidine kinase KdpD
D: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,60812
Polymers43,2922
Non-polymers1,31610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-100 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.470, 92.710, 174.522
Angle α, β, γ (deg.)90.00, 93.39, 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 Osmosensitive K+ channel histidine kinase KdpD


Mass: 29378.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: Tmari_0855 / Production host: Escherichia coli (E. coli)
References: UniProt: R4NPW0, UniProt: Q9WZV7*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#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 (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0468 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYT9

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Non-polymers , 5 types, 320 molecules

#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.: 13 / 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: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1,8M HH4SO4, 0,1M citrato 7,5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97927 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.2→87.11 Å / Num. obs: 55215 / % possible obs: 99.8 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.6
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.539 / Num. unique obs: 4509

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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: 2.2→87.11 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 11.516 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22694 2793 5.1 %RANDOM
Rwork0.18551 ---
obs0.18767 52418 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.273 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å20.44 Å2
2--2.31 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→87.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 134 309 5979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195768
X-RAY DIFFRACTIONr_bond_other_d0.0030.025470
X-RAY DIFFRACTIONr_angle_refined_deg2.0332.0057837
X-RAY DIFFRACTIONr_angle_other_deg1.111312667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.80725.021239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.881151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7631529
X-RAY DIFFRACTIONr_chiral_restr0.120.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026225
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021074
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_it2.0463.6462854
X-RAY DIFFRACTIONr_mcbond_other2.0463.6452853
X-RAY DIFFRACTIONr_mcangle_it3.0595.4563562
X-RAY DIFFRACTIONr_mcangle_other3.0595.4573563
X-RAY DIFFRACTIONr_scbond_it3.0924.0872914
X-RAY DIFFRACTIONr_scbond_other3.0864.0832906
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.675.9954266
X-RAY DIFFRACTIONr_long_range_B_refined6.55243.896301
X-RAY DIFFRACTIONr_long_range_B_other6.55343.9086302
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 216 -
Rwork0.261 3852 -
obs--99.78 %
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)
11.62440.81391.14892.01612.70534.8512-0.00960.2833-0.32210.108-0.05510.11390.4628-0.18730.06470.0921-0.04880.00230.0868-0.08240.1152-8.2309-43.0082-34.8178
21.72180.9292-1.33772.0796-2.42054.1380.00340.24590.32820.116-0.0681-0.0842-0.46930.19130.06470.1014-0.0583-0.02910.08450.08370.108113.5954-18.1745-34.8573
33.6721-0.86591.27843.1467-1.38596.0291-0.0838-0.14250.34960.14940.36420.3878-0.7034-0.6974-0.28040.08340.08190.04080.09980.06540.1208-17.267-16.7294-21.4579
43.8793-0.9893-1.37533.10151.64475.1038-0.068-0.2147-0.36460.16810.3389-0.44710.59180.7152-0.2710.07340.0901-0.04420.1324-0.0630.14622.4934-44.7132-21.4605
500000000000000-00.092000.09200.092000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A243 - 501
2X-RAY DIFFRACTION2B244 - 501
3X-RAY DIFFRACTION3C2 - 123
4X-RAY DIFFRACTION4D2 - 123

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