[English] 日本語
Yorodumi
- PDB-6p7t: Crystal structure of apo ToxT K231A from Vibrio cholerae strain SCE256 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p7t
TitleCrystal structure of apo ToxT K231A from Vibrio cholerae strain SCE256
ComponentsToxin co-regulated pilus virulence regulatory protein
KeywordsDNA BINDING PROTEIN / AraC / XylS / virulence regulation / cholerae
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
ToxT, HTH1 motif / Jelly Rolls - #810 / ToxT, HTH1 motif superfamily / Bacterial regulatory helix-turn-helix proteins, AraC family / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. ...ToxT, HTH1 motif / Jelly Rolls - #810 / ToxT, HTH1 motif superfamily / Bacterial regulatory helix-turn-helix proteins, AraC family / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Toxin co-regulated pilus virulence regulatory protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsCruite, J.T. / Kull, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI120068 United States
CitationJournal: Commun Biol / Year: 2019
Title: Structural basis for virulence regulation inVibrio choleraeby unsaturated fatty acid components of bile.
Authors: Cruite, J.T. / Kovacikova, G. / Clark, K.A. / Woodbrey, A.K. / Skorupski, K. / Kull, F.J.
History
DepositionJun 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Toxin co-regulated pilus virulence regulatory protein


Theoretical massNumber of molelcules
Total (without water)32,1631
Polymers32,1631
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.800, 45.500, 77.000
Angle α, β, γ (deg.)90.000, 97.700, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Toxin co-regulated pilus virulence regulatory protein


Mass: 32163.098 Da / Num. of mol.: 1 / Mutation: K231A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: tcpN / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F5Q9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate, 20% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→26.55 Å / Num. obs: 9665 / % possible obs: 99.82 % / Redundancy: 6.7 % / Biso Wilson estimate: 71.58 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08283 / Rpim(I) all: 0.03474 / Rrim(I) all: 0.08999 / Net I/σ(I): 12.35
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.6972 / Mean I/σ(I) obs: 2.81 / Num. unique obs: 960 / CC1/2: 0.859 / Rpim(I) all: 0.292 / Rrim(I) all: 0.757 / % possible all: 99.69

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→26.55 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.28 / Phase error: 34
RfactorNum. reflection% reflection
Rfree0.2867 967 10.01 %
Rwork0.2455 --
obs0.2497 9664 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.51 Å2 / Biso mean: 80.8288 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.5→26.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 0 24 2241
Biso mean---75.42 -
Num. residues----271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.63170.36361370.353212291366
2.6317-2.79650.38131350.325612131348
2.7965-3.01220.40971380.316512481386
3.0122-3.31490.32911380.305112441382
3.3149-3.79360.31011380.260112401378
3.7936-4.77580.27881360.213112261362
4.7758-28.38730.2311450.216212971442

+
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