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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uqt
TitleClostridium difficile Toxin B (TcdB) glucosyltransferase domain co-crystallized with apigenin
ComponentsToxin B
KeywordsTRANSFERASE / glucosyltransferase / toxin
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-AGI / : / Toxin B
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsAlvin, J.W. / Lacy, D.B.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Veterans AffairsBx002943 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 / 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

-
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)131,0945
Polymers130,7142
Non-polymers3803
Water00
1
A: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4122
Polymers65,3571
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6823
Polymers65,3571
Non-polymers3252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.090, 154.810, 271.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Toxin B


Mass: 65356.988 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AGI / 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one / Apigenin


Mass: 270.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O5

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5-8.5, 0.2 M Mg(CH3CHOO)2, PEG 3350 5-25%

-
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: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.75→44.437 Å / Num. obs: 45388 / % possible obs: 99.75 % / Redundancy: 6.6 % / CC1/2: 0.549 / Net I/σ(I): 21.33

-
Processing

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

2bvm


Resolution: 2.75→44.437 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 1978 4.37 %
Rwork0.1964 --
obs0.1981 45276 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→44.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8820 0 22 0 8842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079004
X-RAY DIFFRACTIONf_angle_d0.90612154
X-RAY DIFFRACTIONf_dihedral_angle_d21.5953393
X-RAY DIFFRACTIONf_chiral_restr0.0531322
X-RAY DIFFRACTIONf_plane_restr0.0061583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.81880.45291370.38683078X-RAY DIFFRACTION100
2.8188-2.8950.36841500.32833006X-RAY DIFFRACTION100
2.895-2.98020.31071280.28173076X-RAY DIFFRACTION100
2.9802-3.07630.29991520.26293055X-RAY DIFFRACTION100
3.0763-3.18630.281300.25223066X-RAY DIFFRACTION100
3.1863-3.31380.28141450.25623070X-RAY DIFFRACTION100
3.3138-3.46460.29011360.22793092X-RAY DIFFRACTION100
3.4646-3.64710.25051450.20633077X-RAY DIFFRACTION100
3.6471-3.87550.24071380.19533088X-RAY DIFFRACTION100
3.8755-4.17450.20341430.17753108X-RAY DIFFRACTION100
4.1745-4.59420.1921480.15783105X-RAY DIFFRACTION100
4.5942-5.25810.20811310.15983110X-RAY DIFFRACTION100
5.2581-6.62120.23141520.20423160X-RAY DIFFRACTION100
6.6212-44.44330.21141430.16623207X-RAY DIFFRACTION97
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)
11.8961-1.6472-0.50153.2168-0.42681.3272-0.3864-0.2273-0.81990.1720.24480.24410.83780.16890.09021.21560.12780.10740.52410.08581.1259109.5164-3.805819.9467
21.6719-0.29310.25881.66140.90022.3114-0.0991-0.13350.17540.1190.0428-0.0096-0.1399-0.30260.08580.44660.0246-0.02630.5078-0.01920.680797.723542.550214.2491
36.90060.46210.83992.6121-1.00773.4621-0.13160.8220.1446-0.30810.1288-0.0594-0.31140.40450.00760.5268-0.0933-0.03410.53540.00730.6736110.281536.287-14.7153
41.6685-0.0729-0.04721.14160.45562.4876-0.0549-0.1879-0.220.15410.1117-0.13650.24810.1456-0.04580.5092-0.0189-0.03730.4417-0.00330.7242107.803127.58912.8327
51.67160.82742.07960.50791.23843.0566-0.1195-0.42220.0251-0.0317-0.07430.4682-0.5308-0.22850.08770.6887-0.10260.01160.8766-0.06940.8211115.634450.71348.3871
61.25040.77210.24740.9494-0.44060.8983-0.34790.0275-0.35920.12920.6287-0.34410.99111.6554-0.31731.39930.766-0.31961.6526-0.35370.9159148.846913.414132.3518
72.1589-1.26970.67853.49330.50094.54730.0775-0.24550.2390.57080.2711-0.2028-0.03921.0705-0.24860.812-0.0351-0.08371.0905-0.29260.7255136.922542.386251.5203
83.24470.3911-0.06630.5070.98052.37940.0841-1.0876-0.78660.4721-0.2479-0.21761.83320.30130.01242.55770.6704-0.49361.4852-0.07620.8476136.959811.135769.8265
94.52-1.24920.59492.701-0.35722.48440.18760.28940.45570.06660.2017-0.76690.73831.3958-0.22590.79450.3694-0.23471.1475-0.30010.5582137.44830.53637.0977
101.8997-1.4060.23735.0505-0.07691.26680.29160.6408-0.52540.1346-0.21250.69360.70530.1176-0.09070.86380.3276-0.16181.1597-0.23290.7442132.548726.029535.8027
111.77920.3440.82150.7148-0.77421.67610.5934-0.09650.06990.0264-0.31050.28830.7111-0.0724-0.29471.30970.1584-0.07781.1488-0.02520.7471127.883925.791454.879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 88 )
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 298 )
3X-RAY DIFFRACTION3chain 'A' and (resid 299 through 339 )
4X-RAY DIFFRACTION4chain 'A' and (resid 340 through 512 )
5X-RAY DIFFRACTION5chain 'A' and (resid 513 through 539 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 137 )
7X-RAY DIFFRACTION7chain 'B' and (resid 138 through 298 )
8X-RAY DIFFRACTION8chain 'B' and (resid 299 through 366 )
9X-RAY DIFFRACTION9chain 'B' and (resid 367 through 438 )
10X-RAY DIFFRACTION10chain 'B' and (resid 439 through 494 )
11X-RAY DIFFRACTION11chain 'B' and (resid 495 through 539 )

+
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