[English] 日本語
Yorodumi
- PDB-9bja: C. difficile Tcdb cysteine protease domain in complex with IP6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bja
TitleC. difficile Tcdb cysteine protease domain in complex with IP6
ComponentsToxin B
KeywordsTOXIN / catalytic activity peptidase activity catalytic activity / acting on a protein toxin activity small molecule binding
Function / homology
Function and homology information


glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis ...glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding
Similarity search - Function
TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. ...TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Toxin B
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVeyron, S. / Cummer, R.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-173262 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-04908 Canada
CitationJournal: Chemrxiv / Year: 2024
Title: Structure-activity relationship of inositol thiophosphate analogs as allosteric activators of Clostridioides difficile Toxin B
Authors: Cummer, R. / Grosjean, F. / Bolteau, R. / Vasegh, S.E. / Veyron, S. / Keogh, L. / Trempe, J.-F. / Castagner, B.
History
DepositionApr 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Toxin B
B: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0494
Polymers59,7292
Non-polymers1,3202
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.051, 89.171, 67.597
Angle α, β, γ (deg.)90.000, 103.780, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 5 through 6 and (name N...
d_2ens_1(chain "B" and (resid 5 through 16 or (resid 17...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASNASNGLNGLNAA5 - 666 - 67
d_12ASNASNPHEPHEAA68 - 11569 - 116
d_13THRTHRTYRTYRAA117 - 160118 - 161
d_14ILEILEARGARGAA162 - 202163 - 203
d_15ASNASNASPASPAA204 - 213205 - 214
d_16SERSERSERSERAA215 - 230216 - 231
d_17LYSLYSPROPROAA232 - 252233 - 253
d_18IHPIHPIHPIHPAC301
d_21ASNASNGLNGLNBB5 - 666 - 67
d_22ASNASNPHEPHEBB68 - 11569 - 116
d_23THRTHRTYRTYRBB117 - 160118 - 161
d_24ILEILEARGARGBB162 - 202163 - 203
d_25ASNASNASPASPBB204 - 213205 - 214
d_26SERSERSERSERBB215 - 230216 - 231
d_27LYSLYSPROPROBB232 - 252233 - 253
d_28IHPIHPIHPIHPBD301

NCS oper: (Code: givenMatrix: (-0.999713018047, 0.023100743894, -0.00634327823668), (0.023280667646, 0.999280837131, -0.0299302365067), (0.00564730565827, -0.0300693228214, -0.999531862305)Vector: 29. ...NCS oper: (Code: given
Matrix: (-0.999713018047, 0.023100743894, -0.00634327823668), (0.023280667646, 0.999280837131, -0.0299302365067), (0.00564730565827, -0.0300693228214, -0.999531862305)
Vector: 29.8692644756, 1.65152705244, -31.7504398893)

-
Components

#1: Protein Toxin B


Mass: 29864.479 Da / Num. of mol.: 2 / Fragment: Cysteine protease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Strain: 342 / Gene: tcdB, toxB / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P18177, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1 M Tris HCl, pH 8.2, 36% (w/v) PEG2000 monomethyl ether

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95371 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 2.1→89.17 Å / Num. obs: 29657 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 34.04 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.048 / Net I/σ(I): 9.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2423 / CC1/2: 0.911 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
BUSTER2.10.4refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→52.87 Å / SU ML: 0.2728 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.4459
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 1496 5.06 %Random
Rwork0.2281 28055 --
obs0.2296 29551 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.25 Å2
Refinement stepCycle: LAST / Resolution: 2.1→52.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3917 0 72 199 4188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00994098
X-RAY DIFFRACTIONf_angle_d1.2095567
X-RAY DIFFRACTIONf_chiral_restr0.0747626
X-RAY DIFFRACTIONf_plane_restr0.015700
X-RAY DIFFRACTIONf_dihedral_angle_d15.85091537
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.5523832412 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.30561410.28982543X-RAY DIFFRACTION100
2.17-2.250.34951200.27822539X-RAY DIFFRACTION99.85
2.25-2.340.32381660.27112531X-RAY DIFFRACTION99.7
2.34-2.440.27211340.26672538X-RAY DIFFRACTION99.7
2.44-2.570.31741290.26592542X-RAY DIFFRACTION99.85
2.57-2.730.2711390.2752554X-RAY DIFFRACTION99.7
2.73-2.940.24711330.2712556X-RAY DIFFRACTION99.19
2.94-3.240.26851180.24892553X-RAY DIFFRACTION99.63
3.24-3.710.25691420.21792546X-RAY DIFFRACTION99.33
3.71-4.670.21481440.18062548X-RAY DIFFRACTION99.74
4.67-52.870.23371300.19482605X-RAY DIFFRACTION99.13

+
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