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- PDB-6rgz: Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 6rgz
TitleRevisiting pH-gated conformational switch. Complex HK853-RR468 pH 6.5
Components
  • Response regulator
  • Sensor histidine kinase
KeywordsSIGNALING PROTEIN / Histidine Kinase / Response Regulator / Phosphotransfer / Phosphatase
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / 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 / 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 / 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: 2.35 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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)88,86623
Polymers86,5834
Non-polymers2,28319
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12860 Å2
ΔGint-297 kcal/mol
Surface area30570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.736, 93.608, 173.927
Angle α, β, γ (deg.)90.00, 93.35, 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 , 5 types, 217 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 198 / 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: 3.25 Å3/Da / Density % sol: 62.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1,8M HH4SO4, 0,1M citrato 6,5

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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: 2.35→28.94 Å / Num. obs: 45694 / % possible obs: 99.2 % / Redundancy: 4.6 % / CC1/2: 0.999 / Net I/σ(I): 13.7
Reflection shellResolution: 2.35→2.43 Å / Num. unique obs: 4320

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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: 2.35→28.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.514 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26512 2190 4.8 %RANDOM
Rwork0.21487 ---
obs0.21728 43450 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.257 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å2-0 Å20.73 Å2
2--2.54 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.35→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5516 0 127 217 5860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195743
X-RAY DIFFRACTIONr_bond_other_d0.0010.025428
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9987810
X-RAY DIFFRACTIONr_angle_other_deg0.892312560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2985717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78124.938241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78815996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5711530
X-RAY DIFFRACTIONr_chiral_restr0.0650.2934
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026225
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021079
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_it0.7853.8362856
X-RAY DIFFRACTIONr_mcbond_other0.7853.8362855
X-RAY DIFFRACTIONr_mcangle_it1.3625.7493565
X-RAY DIFFRACTIONr_mcangle_other1.3615.753566
X-RAY DIFFRACTIONr_scbond_it0.8554.0262887
X-RAY DIFFRACTIONr_scbond_other0.8353.9182830
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4045.8444158
X-RAY DIFFRACTIONr_long_range_B_refined5.69145.3956112
X-RAY DIFFRACTIONr_long_range_B_other5.51345.0436066
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 173 -
Rwork0.285 3133 -
obs--98.33 %
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)
11.64120.9717-1.14112.4853-2.85355.12090.00050.26420.37430.1327-0.1548-0.1909-0.52830.49740.15430.0862-0.0881-0.0170.1510.11760.1761-20.8421-3.643-34.684
21.68660.7040.89132.56133.4466.25450.00970.3384-0.4590.2363-0.21810.1830.6776-0.58150.20840.103-0.09530.02310.1711-0.14180.1888-42.4876-28.9697-34.3861
34.7816-1.93041.05254.221-2.04357.2996-0.0795-0.10990.34230.33310.59070.6405-0.9071-1.0224-0.51120.11640.13750.08850.17680.14190.2085-51.6796-1.8982-21.2722
44.8987-1.6155-1.24524.43712.58816.7885-0.1795-0.3046-0.38450.33260.604-0.54330.73541.0973-0.42450.0840.1366-0.05730.2504-0.1230.1744-12.0099-30.4643-21.0094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A243 - 479
2X-RAY DIFFRACTION2B246 - 478
3X-RAY DIFFRACTION3C2 - 122
4X-RAY DIFFRACTION4D1 - 122

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