[English] 日本語
Yorodumi
- PDB-6rh8: Revisiting pH-gated conformational switch. Complex HK853 mutant H... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rh8
TitleRevisiting pH-gated conformational switch. Complex HK853 mutant H260A -RR468 mutant D53A pH 5.3
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: 1.9 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 19, 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)88,91125
Polymers86,2314
Non-polymers2,68021
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13320 Å2
ΔGint-305 kcal/mol
Surface area31400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.547, 92.189, 175.015
Angle α, β, γ (deg.)90.00, 93.61, 90.00
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein Sensor histidine kinase


Mass: 29311.215 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 (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
#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.: 19 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.3 / Details: 1,2M NH4SO4, 0,1M BisTris pH 5.3

-
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: 1.9→87.33 Å / Num. obs: 84541 / % possible obs: 98.8 % / Redundancy: 6.2 % / CC1/2: 0.998 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 4396

-
Processing

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

3dge


Resolution: 1.9→87.33 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.931 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.12 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21924 4149 4.9 %RANDOM
Rwork0.1772 ---
obs0.17929 80390 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.074 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20.77 Å2
2--1.43 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→87.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5698 0 149 501 6348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195940
X-RAY DIFFRACTIONr_bond_other_d0.0020.025712
X-RAY DIFFRACTIONr_angle_refined_deg1.9942.0138041
X-RAY DIFFRACTIONr_angle_other_deg1.092313277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4725.135259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.412151123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.261533
X-RAY DIFFRACTIONr_chiral_restr0.1390.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026307
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021092
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_it4.2854.1792864
X-RAY DIFFRACTIONr_mcbond_other4.284.1762863
X-RAY DIFFRACTIONr_mcangle_it5.5686.2343574
X-RAY DIFFRACTIONr_mcangle_other5.576.2373575
X-RAY DIFFRACTIONr_scbond_it5.6564.9463076
X-RAY DIFFRACTIONr_scbond_other5.3844.8662997
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0697.0194346
X-RAY DIFFRACTIONr_long_range_B_refined10.40750.8766634
X-RAY DIFFRACTIONr_long_range_B_other10.40650.8726635
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 317 -
Rwork0.262 5821 -
obs--97.93 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more