[English] 日本語
Yorodumi
- PDB-7n0e: Co-complex of the histidine kinase region of RetS and the dimeriz... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n0e
TitleCo-complex of the histidine kinase region of RetS and the dimerization and histidine phosphotransfer domain of GacS
Components(Histidine kinase) x 2
KeywordsSIGNALING PROTEIN / Co-complex
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020
Similarity search - Function
7TM-DISM receptor, extracellular domain, type 2 / 7TM-DISM receptor, extracellular domain, type 1 / 7TM diverse intracellular signalling / 7TMR-DISM extracellular 2 / 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 ...7TM-DISM receptor, extracellular domain, type 2 / 7TM-DISM receptor, extracellular domain, type 1 / 7TM diverse intracellular signalling / 7TMR-DISM extracellular 2 / 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. / 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
Similarity search - Domain/homology
: / Histidine kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRyan Kaler, K. / Schubot, F.D. / Nix, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: RetS inhibits Pseudomonas aeruginosa biofilm formation by disrupting the canonical histidine kinase dimerization interface of GacS.
Authors: Ryan Kaler, K.M. / Nix, J.C. / Schubot, F.D.
History
DepositionMay 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Histidine kinase
A: Histidine kinase


Theoretical massNumber of molelcules
Total (without water)31,6262
Polymers31,6262
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-35 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.360, 103.360, 61.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-714-

HOH

-
Components

#1: Protein Histidine kinase /


Mass: 24854.898 Da / Num. of mol.: 1 / Fragment: residues 414-639
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: GNQ20_09825 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A9JSD6, histidine kinase
#2: Protein Histidine kinase /


Mass: 6770.674 Da / Num. of mol.: 1 / Fragment: residues 121-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: C0044_06730 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V3GQV5, histidine kinase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium sulfate, 0.1 M tris pH 8.5, 30% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97625 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 20, 2019
Details: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.29→44.76 Å / Num. obs: 17507 / % possible obs: 100 % / Redundancy: 21.1 % / CC1/2: 1 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.033 / Rrim(I) all: 0.15 / Net I/σ(I): 16.9 / Num. measured all: 369869
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.29-2.3721.19.9917080.3973.04514.059100
8.87-44.7619.50.02334110.0050.02499.2

-
Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DK7

6dk7


Resolution: 2.3→39.69 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 939 5.63 %
Rwork0.2475 15736 -
obs0.2486 16675 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.1 Å2 / Biso mean: 89.5913 Å2 / Biso min: 38.92 Å2
Refinement stepCycle: final / Resolution: 2.3→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 0 20 1986
Biso mean---78.57 -
Num. residues----255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.420.42231080.38241772188077
2.42-2.570.3291320.327322802412100
2.57-2.770.32611360.320722822418100
2.77-3.050.32451420.29623162458100
3.05-3.490.27221360.281123132449100
3.49-4.40.24761380.231423502488100
4.4-39.690.23921470.212824232570100
Refinement TLS params.Method: refined / Origin x: -37.4857 Å / Origin y: -17.0119 Å / Origin z: 0.8211 Å
111213212223313233
T0.5385 Å20.0707 Å2-0.0682 Å2-0.4808 Å20.043 Å2--0.3982 Å2
L3.1299 °21.9799 °2-1.1074 °2-3.9377 °2-0.6129 °2--1.4921 °2
S-0.0329 Å °-0.1467 Å °0.116 Å °0.1705 Å °-0.0641 Å °-0.5636 Å °0.029 Å °0.1045 Å °0.0801 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB415 - 639
2X-RAY DIFFRACTION1allA285 - 344
3X-RAY DIFFRACTION1allS1 - 20

+
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