[English] 日本語
Yorodumi
- PDB-3o1i: Crystal Structure of the TorS sensor domain - TorT complex in the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o1i
TitleCrystal Structure of the TorS sensor domain - TorT complex in the absence of ligand
Components
  • Periplasmic protein TorT
  • Sensor protein TorS
KeywordsSIGNALING PROTEIN / Ligand free / Two component sensor / Periplasmic binding protein / TMAO
Function / homology
Function and homology information


cellular hyperosmotic response / histidine kinase / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / identical protein binding / plasma membrane
Similarity search - Function
TMAO reductase system, periplasmic protein TorT / Signal transduction histidine kinase, TMAO sensor TorS / Sensor protein TorS, sensor domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #920 / Sensor histidine kinase TorS, sensor domain / TorS, sensor domain superfamily / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. ...TMAO reductase system, periplasmic protein TorT / Signal transduction histidine kinase, TMAO sensor TorS / Sensor protein TorS, sensor domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #920 / Sensor histidine kinase TorS, sensor domain / TorS, sensor domain superfamily / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / HAMP domain profile. / HAMP domain / 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 / Response regulator / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Periplasmic binding protein-like I / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Phosphorelay protein LuxU / Periplasmic protein TorT
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMoore, J.O. / Hendrickson, W.A.
CitationJournal: Structure / Year: 2012
Title: An asymmetry-to-symmetry switch in signal transmission by the histidine kinase receptor for TMAO.
Authors: Moore, J.O. / Hendrickson, W.A.
History
DepositionJul 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Mar 27, 2013Group: Other
Revision 1.3Apr 3, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sensor protein TorS
B: Sensor protein TorS
D: Periplasmic protein TorT
C: Periplasmic protein TorT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5335
Polymers131,1784
Non-polymers3541
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.710, 364.520, 80.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Sensor protein TorS


Mass: 31701.875 Da / Num. of mol.: 2 / Fragment: Sensor Domain (UNP residues 51-323)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: EB10 / Gene: TorS, VPA0675 / Plasmid: pRSFDuet-t / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q87ID1, histidine kinase
#2: Protein Periplasmic protein TorT


Mass: 33887.172 Da / Num. of mol.: 2 / Fragment: UNP residues 31-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: EB10 / Gene: TorT, VPA0674 / Plasmid: pETDuet-t / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB DE3 pLysS / References: UniProt: Q87ID2
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1-4% PEG 400, 1.0-1.7M AmSO4, 100mM Tris pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.98009 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2007 / Details: slits and mirrors
RadiationMonochromator: horizontally deflecting and focusing crystal preceded by a vertically focusing mirror.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98009 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 42656 / Num. obs: 42602 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.141 / Rsym value: 0.128 / Net I/σ(I): 11.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.455 / Rsym value: 0.421 / % possible all: 9.8

-
Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Isopropanol bound structure

Resolution: 2.8→19.93 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2050435.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.291 2107 5 %RANDOM
Rwork0.248 ---
obs0.248 42485 99.8 %-
all-42677 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.941 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 65.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.55 Å20 Å2
3----1.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9017 0 21 98 9136
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.62.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 365 5.3 %
Rwork0.343 6583 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3Peg40014C.paramPeg40014C.top

+
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://pdbjlvh1.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