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- PDB-6rfv: Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 7 -

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Basic information

Entry
Database: PDB / ID: 6rfv
TitleRevisiting pH-gated conformational switch. Complex HK853-RR468 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 / 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 / Response regulator / histidine kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsMideros-Mora, C. / Casino, P. / Marina, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministry of Economy and CompetitivenessBIO2016-78571-P Spain
Spanish Ministry of Economy and CompetitivenessBFU2016-78606-P Spain
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 16, 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: Sensor histidine kinase
B: Sensor histidine kinase
C: Response regulator
D: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,83122
Polymers86,5834
Non-polymers2,24818
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12340 Å2
ΔGint-279 kcal/mol
Surface area30030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.673, 93.579, 172.703
Angle α, β, γ (deg.)90.00, 93.32, 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
Details: Some residues remain as Alanine in the .pdb because the side chain can not be traced
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (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 (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0468 / Variant: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYT9

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Non-polymers , 4 types, 174 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.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg / Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 61.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1,8 M HH4SO4, 0,1 M citrato pH 7

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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: 2.83→28.76 Å / Num. obs: 24854 / % possible obs: 95 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 6
Reflection shellResolution: 2.83→2.98 Å / Rmerge(I) obs: 0.451 / Num. unique obs: 3270

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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: 2.83→30 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.861 / SU B: 40.066 / SU ML: 0.423 / Cross valid method: THROUGHOUT / ESU R: 2.518 / ESU R Free: 0.448 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30923 1189 4.8 %RANDOM
Rwork0.24284 ---
obs0.24606 23662 95.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.463 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å20 Å20.4 Å2
2--2 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.83→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5481 0 134 172 5787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195709
X-RAY DIFFRACTIONr_bond_other_d0.0020.025377
X-RAY DIFFRACTIONr_angle_refined_deg1.5712.0027756
X-RAY DIFFRACTIONr_angle_other_deg0.992312456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0475706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.08925.167240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.166151004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4581527
X-RAY DIFFRACTIONr_chiral_restr0.080.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026157
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021060
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_it0.9563.4212824
X-RAY DIFFRACTIONr_mcbond_other0.9563.4212823
X-RAY DIFFRACTIONr_mcangle_it1.6675.1313524
X-RAY DIFFRACTIONr_mcangle_other1.6675.1313525
X-RAY DIFFRACTIONr_scbond_it1.0033.6222885
X-RAY DIFFRACTIONr_scbond_other0.8743.5022824
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4965.234141
X-RAY DIFFRACTIONr_long_range_B_refined4.9740.6666214
X-RAY DIFFRACTIONr_long_range_B_other4.52140.5446193
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.831→2.904 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 67 -
Rwork0.344 1335 -
obs--74.22 %
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)
11.82631.18021.68883.26063.84686.17620.10920.3599-0.36730.2278-0.26590.21690.6849-0.69910.15670.1381-0.12690.03290.3229-0.14520.2078-8.459-43.9158-34.037
21.45841.2415-1.73242.6832-2.95185.57250.04260.18120.30570.0596-0.2283-0.1611-0.55080.61110.18570.1418-0.0842-0.03680.26330.13660.224813.4282-18.2608-33.8156
35.6438-1.55642.06524.3806-2.71876.8675-0.3963-0.15730.5450.34640.84230.7645-0.7549-1.1118-0.4460.09130.12320.03420.24980.19330.2728-17.5312-16.6305-21.2415
46.6086-3.2754-2.60313.46282.66326.2041-0.4063-0.4822-0.4840.45520.8768-0.59410.73111.3698-0.47050.09660.1812-0.08830.3759-0.26050.41422.3322-45.4009-21.0056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A246 - 478
2X-RAY DIFFRACTION2B247 - 478
3X-RAY DIFFRACTION3C2 - 121
4X-RAY DIFFRACTION4D2 - 122

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