[English] 日本語
Yorodumi
- PDB-7d6q: Crystal structure of the Stx2a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d6q
TitleCrystal structure of the Stx2a
Components
  • Shiga toxin 2 B subunit
  • rRNA N-glycosylase
KeywordsTOXIN / Shiga toxin
Function / homology
Function and homology information


symbiont-mediated hemolysis of host erythrocyte / rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation / extracellular region
Similarity search - Function
Shiga-like toxin, subunit A / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Enterotoxin / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein
Similarity search - Domain/homology
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / Shiga toxin 2 B subunit / rRNA N-glycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTakahashi, M. / Tamada, M. / Hibino, M. / Senda, M. / Okuda, A. / Miyazawa, A. / Senda, T. / Nishikawa, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP19am0101001 Japan
CitationJournal: Commun Biol / Year: 2021
Title: Identification of a peptide motif that potently inhibits two functionally distinct subunits of Shiga toxin.
Authors: Watanabe-Takahashi, M. / Tamada, M. / Senda, M. / Hibino, M. / Shimizu, E. / Okuta, A. / Miyazawa, A. / Senda, T. / Nishikawa, K.
History
DepositionOct 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: 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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: rRNA N-glycosylase
B: Shiga toxin 2 B subunit
C: Shiga toxin 2 B subunit
D: Shiga toxin 2 B subunit
E: Shiga toxin 2 B subunit
F: Shiga toxin 2 B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,15610
Polymers72,3516
Non-polymers8054
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12920 Å2
ΔGint-16 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.695, 146.695, 60.875
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

#1: Protein rRNA N-glycosylase / Shiga toxin 2 A subunit


Mass: 33228.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: stx2a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XBV2, rRNA N-glycosylase
#2: Protein
Shiga toxin 2 B subunit


Mass: 7824.590 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: stxII, stx2B, stx2B_2, stx2dB, stx2vB, stxB2, vtx2B / Production host: Escherichia coli (E. coli) / References: UniProt: Q7DJJ2
#3: Chemical
ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H11NO3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4 M sodium formate, 100 mM MES pH 6.5, 50 mM 3-(1-Pyridinio)-1-propanesulfonate (PPS)

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 4, 2018
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.02 Å / Num. obs: 69387 / % possible obs: 100 % / Redundancy: 21.2 % / Biso Wilson estimate: 15.28 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 25.09
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 6.62 / Num. unique obs: 10290

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MOLREPphasing
PHENIX1.14_3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R4P

1r4p


Resolution: 1.8→48.02 Å / SU ML: 0.154 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.2225
RfactorNum. reflection% reflection
Rfree0.1903 3470 5 %
Rwork0.1627 --
obs0.1641 69378 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4916 0 52 465 5433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00655090
X-RAY DIFFRACTIONf_angle_d0.77146904
X-RAY DIFFRACTIONf_chiral_restr0.0557778
X-RAY DIFFRACTIONf_plane_restr0.0048885
X-RAY DIFFRACTIONf_dihedral_angle_d2.87243621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.22251380.18622612X-RAY DIFFRACTION100
1.82-1.850.23561370.18812608X-RAY DIFFRACTION99.96
1.85-1.880.23351370.18142610X-RAY DIFFRACTION100
1.88-1.910.23011400.18432657X-RAY DIFFRACTION99.96
1.91-1.940.21061350.17342570X-RAY DIFFRACTION100
1.94-1.970.21151390.16642625X-RAY DIFFRACTION100
1.97-2.010.2241390.16322649X-RAY DIFFRACTION100
2.01-2.050.19261370.17132604X-RAY DIFFRACTION100
2.05-2.090.20231400.16232652X-RAY DIFFRACTION100
2.09-2.130.1751370.15742608X-RAY DIFFRACTION100
2.13-2.180.1891390.15452635X-RAY DIFFRACTION100
2.18-2.240.17951380.15362623X-RAY DIFFRACTION100
2.24-2.30.1931380.16132630X-RAY DIFFRACTION100
2.3-2.370.22021390.15912632X-RAY DIFFRACTION100
2.37-2.440.20911400.16492660X-RAY DIFFRACTION100
2.44-2.530.21971360.17262599X-RAY DIFFRACTION100
2.53-2.630.22131400.17792643X-RAY DIFFRACTION100
2.63-2.750.20411370.17992620X-RAY DIFFRACTION100
2.75-2.90.18561400.17472655X-RAY DIFFRACTION100
2.9-3.080.18821380.17262627X-RAY DIFFRACTION100
3.08-3.320.19911400.1672649X-RAY DIFFRACTION100
3.32-3.650.17631400.15392654X-RAY DIFFRACTION100
3.65-4.180.1421400.14152675X-RAY DIFFRACTION100
4.18-5.260.15391410.13032670X-RAY DIFFRACTION100
5.26-48.020.18851450.17962741X-RAY DIFFRACTION99.72

+
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