[English] 日本語
Yorodumi
- PDB-3srz: Clostridium difficile toxin A (TcdA) glucolsyltransferase domain ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3srz
TitleClostridium difficile toxin A (TcdA) glucolsyltransferase domain bound to UDP-glucose
ComponentsToxin A
KeywordsTRANSFERASE / Glucosyltransferase
Function / homology
Function and homology information


host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / 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 ...host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / 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 / plasma membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1190 / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1190 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Toxin A / Toxin A
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsPruitt, R.N. / Chumbler, N.M. / Farrow, M.A. / Seeback, S.A. / Friedman, D.B. / Spiller, B.W. / Lacy, D.B.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Determinants of Clostridium difficile Toxin A Glucosyltransferase Activity.
Authors: Pruitt, R.N. / Chumbler, N.M. / Rutherford, S.A. / Farrow, M.A. / Friedman, D.B. / Spiller, B. / Lacy, D.B.
History
DepositionJul 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Toxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0213
Polymers64,4001
Non-polymers6212
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.779, 141.779, 63.351
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Toxin A


Mass: 64399.672 Da / Num. of mol.: 1 / Fragment: glucosyltransferase domain (UNP residues 1-542)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD0663, CD630_06630, tcdA / Plasmid: pC-His1622 / Production host: Bacillus megaterium (bacteria) / Strain (production host): WH320
References: UniProt: Q189K5, UniProt: P16154*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG6000, 0.1 M bicine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0094 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2010
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0094 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. all: 23085 / Num. obs: 23039 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.5
Reflection shellResolution: 2.58→2.67 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2278 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→40.928 Å / SU ML: 0.87 / Isotropic thermal model: ISOTROPIC / σ(F): 0 / σ(I): 0 / Phase error: 25.29 / Stereochemistry target values: ML / Details: PDB ENTRY 3SS1
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1914 8.62 %5% THROUGHOUT
Rwork0.1774 ---
all0.1835 23085 --
obs0.1835 22207 96.16 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.25 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4957 Å2-0 Å2-0 Å2
2--4.4957 Å2-0 Å2
3----0.8231 Å2
Refine analyzeLuzzati d res low obs: 49 Å / Luzzati sigma a obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.58→40.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4403 0 37 109 4549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074521
X-RAY DIFFRACTIONf_angle_d1.0876111
X-RAY DIFFRACTIONf_dihedral_angle_d16.7131718
X-RAY DIFFRACTIONf_chiral_restr0.068687
X-RAY DIFFRACTIONf_plane_restr0.004775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5804-2.64490.38641170.28311279X-RAY DIFFRACTION85
2.6449-2.71640.34391250.24711359X-RAY DIFFRACTION90
2.7164-2.79630.30411310.21891388X-RAY DIFFRACTION94
2.7963-2.88660.28631410.22251393X-RAY DIFFRACTION93
2.8866-2.98970.32541290.21111426X-RAY DIFFRACTION96
2.9897-3.10940.33421400.22321425X-RAY DIFFRACTION95
3.1094-3.25080.31041390.2011470X-RAY DIFFRACTION98
3.2508-3.42210.26021360.1891457X-RAY DIFFRACTION98
3.4221-3.63640.24551420.1841510X-RAY DIFFRACTION99
3.6364-3.9170.24041400.17781484X-RAY DIFFRACTION99
3.917-4.31080.22821490.14791511X-RAY DIFFRACTION100
4.3108-4.93370.16871420.12461503X-RAY DIFFRACTION100
4.9337-6.21240.23831400.17151537X-RAY DIFFRACTION100
6.2124-40.93320.19741430.15121551X-RAY DIFFRACTION99
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)
14.05651.29042.11041.72710.0753.36730.07830.0326-0.0114-0.04590.17740.26250.3193-0.3544-0.19930.10090.0673-0.07520.27620.08480.0954-72.6672-51.7446-25.0266
21.58870.16320.45711.3947-0.32871.7102-0.05770.10390.2044-0.0685-0.0915-0.2096-0.33130.35320.03760.1-0.0515-0.10530.03120.10850.1553-29.9081-41.8312-5.2902
31.68841.0856-0.40081.41360.59721.1872-0.13260.56520.4816-0.45740.2480.018-0.64030.1243-0.13510.5103-0.0782-0.04860.3760.15210.2858-32.1984-30.0861-29.9217
41.6907-0.73411.74451.9142-0.96861.96890.14570.2528-0.0386-0.1581-0.1171-0.04690.03190.1612-0.03290.14420.08820.05410.2022-0.01260.1115-43.0382-55.2475-13.458
51.204-0.91991.05981.2959-1.03791.0207-0.2344-0.3405-0.85220.1492-0.1192-0.20470.21990.72940.42120.39710.12320.19440.82080.30460.6117-20.1571-47.1288-18.9252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:87)
2X-RAY DIFFRACTION2(chain A and resid 88:298)
3X-RAY DIFFRACTION3(chain A and resid 299:390)
4X-RAY DIFFRACTION4(chain A and resid 391:506)
5X-RAY DIFFRACTION5(chain A and resid 507:538)

+
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