[English] 日本語
Yorodumi
- PDB-5uqn: Clostridium difficile Toxin B (TcdB) glucosyltransferase domain i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uqn
TitleClostridium difficile Toxin B (TcdB) glucosyltransferase domain in complex with U2F
ComponentsToxin B
KeywordsTRANSFERASE / Glucosyltransferase / Toxin / HYDROLASE
Function / homology
Function and homology information


symbiont-mediated perturbation of host actin cytoskeleton via filamentous actin depolymerization / glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane ...symbiont-mediated perturbation of host actin cytoskeleton via filamentous actin depolymerization / glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / 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 / metal ion binding / membrane
Similarity search - Function
Arc Repressor Mutant, subunit A - #1780 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1190 / Membrane Localization 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 ...Arc Repressor Mutant, subunit A - #1780 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1190 / Membrane Localization 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 / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Arc Repressor Mutant, subunit A / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Chem-U2F / Toxin B
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsAlvin, J.W. / Lacy, D.B.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Veterans AffairsBX02943 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095755 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008320 United States
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Clostridium difficile toxin glucosyltransferase domains in complex with a non-hydrolyzable UDP-glucose analogue.
Authors: Alvin, J.W. / Lacy, D.B.
History
DepositionFeb 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1725
Polymers65,3571
Non-polymers8154
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-34 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.390, 62.390, 328.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Toxin B


Mass: 65356.988 Da / Num. of mol.: 1 / Fragment: residues 1-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: toxB, tcdB / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: P18177, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23FN2O16P2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.44 Å3/Da / Density % sol: 49.63 % / Description: Short bars.
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, 0.2 M ammonium sulfate, PEG 8k 16-34% / PH range: 6-6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.06→54.67 Å / Num. obs: 41228 / % possible obs: 99.1 % / Redundancy: 11.2 % / CC1/2: 0.946 / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.2

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BVL

2bvl


Resolution: 2.06→54.19 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 2000 4.87 %
Rwork0.203 --
obs0.2044 41070 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→54.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4429 0 47 238 4714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084644
X-RAY DIFFRACTIONf_angle_d1.0156294
X-RAY DIFFRACTIONf_dihedral_angle_d15.1462833
X-RAY DIFFRACTIONf_chiral_restr0.051688
X-RAY DIFFRACTIONf_plane_restr0.004815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.11150.29971300.26352544X-RAY DIFFRACTION93
2.1115-2.16860.30031350.26132634X-RAY DIFFRACTION96
2.1686-2.23240.28631400.24572738X-RAY DIFFRACTION99
2.2324-2.30450.25911410.22482748X-RAY DIFFRACTION99
2.3045-2.38690.30991410.22642764X-RAY DIFFRACTION100
2.3869-2.48240.25241420.22582768X-RAY DIFFRACTION100
2.4824-2.59540.22181440.22152815X-RAY DIFFRACTION100
2.5954-2.73220.26031410.22282764X-RAY DIFFRACTION100
2.7322-2.90340.26631430.22292797X-RAY DIFFRACTION100
2.9034-3.12760.23161450.20942837X-RAY DIFFRACTION100
3.1276-3.44230.24051440.21272820X-RAY DIFFRACTION100
3.4423-3.94020.21371470.18292863X-RAY DIFFRACTION100
3.9402-4.96380.17151480.15812903X-RAY DIFFRACTION99
4.9638-54.20840.23941590.1923075X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0653-0.1752-0.52230.8661-0.2850.89890.12320.49610.1672-0.1022-0.2326-0.2224-0.29890.736-0.01190.2548-0.15740.01660.84560.14050.325521.961713.4037-33.9864
20.5333-0.1660.1110.76210.41981.54880.00860.2993-0.0934-0.0413-0.10060.0428-0.06160.06660.08220.1597-0.0256-0.01360.3395-0.05160.27123.15660.2437-25.1745
31.0761-0.7804-0.62672.0569-0.81321.8477-0.1408-0.06190.68760.0665-0.04720.5404-0.5772-0.567600.4010.1476-0.1080.3835-0.15410.6223-15.004424.5176-2.9284
40.92870.00510.22411.12050.33681.8834-0.07230.2833-0.1678-0.02330.0018-0.02240.18850.42780.03670.1309-0.01770.01190.36680.00370.271912.383-7.0832-21.1422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 358 )
2X-RAY DIFFRACTION2chain 'A' and (resid 359 through 542 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2 through 62 )
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 264 )

+
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