[English] 日本語
Yorodumi
- PDB-3ess: Catalytic fragment of Cholix toxin from Vibrio Cholerae in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ess
TitleCatalytic fragment of Cholix toxin from Vibrio Cholerae in complex with the 1,8-Naphthalimide inhibitor
ComponentsCholix toxin
KeywordsTRANSFERASE / TOXIN / ADP-ribosyl transferase / Domain III (C-terminal catalytic domain) / alpha-beta complex
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity
Similarity search - Function
Exotoxin A catalytic domain / Exotoxin A, binding / Exotoxin A, middle domain / Exotoxin A, middle domain superfamily / Exotoxin A catalytic / Exotoxin A binding / Exotoxin A, targeting / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Concanavalin A-like lectin/glucanase domain superfamily ...Exotoxin A catalytic domain / Exotoxin A, binding / Exotoxin A, middle domain / Exotoxin A, middle domain superfamily / Exotoxin A catalytic / Exotoxin A binding / Exotoxin A, targeting / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
1H-benzo[de]isoquinoline-1,3(2H)-dione / Cholix toxin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.191 Å
AuthorsMerrill, A.R. / Jorgensen, R.
CitationJournal: Fems Microbiol.Lett. / Year: 2009
Title: Yeast as a tool for characterizing mono-ADP-ribosyltransferase toxins
Authors: Turgeon, Z. / White, D. / Jorgensen, R. / Visschedyk, D. / Fieldhouse, R.J. / Mangroo, D. / Merrill, A.R.
History
DepositionOct 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 25, 2015Group: Derived calculations
Revision 1.3Sep 6, 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 / 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 / _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: Cholix toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7492
Polymers25,5521
Non-polymers1971
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.590, 64.830, 91.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cholix toxin


Mass: 25552.189 Da / Num. of mol.: 1
Fragment: C-terminal catalytic domain (UNP residues 459 to 665)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: TP / Gene: chxA, toxA / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q5EK40, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-18N / 1H-benzo[de]isoquinoline-1,3(2H)-dione / 1,8-NAPHTHALIMIDE


Mass: 197.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H7NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 15% PEG-8000, 0.02 M KH2PO4, Sitting drop, pH 7.0, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 16, 2008
Details: White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM), vertically focusing mirror (VFM)
RadiationMonochromator: White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM), vertically focusing mirror (VFM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.19→19.55 Å / Num. all: 68749 / Num. obs: 68071 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 13.96 % / Biso Wilson estimate: 10.833 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 18.67
Reflection shellResolution: 1.19→1.22 Å / Redundancy: 10.15 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 5.1 / Num. measured obs: 44204 / Num. unique all: 5012 / Num. unique obs: 4357 / % possible all: 86.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.27 Å19.55 Å
Translation1.27 Å19.55 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MacromolecularCrystallography Data Collection (MXDC) GUIdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q6M

2q6m


Resolution: 1.191→19.551 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.94 / SU ML: 0.08 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.154 2067 3.04 %Random
Rwork0.131 ---
obs0.132 68071 99.04 %-
all-68749 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.987 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 41.46 Å2 / Biso mean: 8.851 Å2 / Biso min: 1.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.475 Å2-0 Å20 Å2
2---1.132 Å2-0 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.191→19.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 0 15 435 2005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091625
X-RAY DIFFRACTIONf_angle_d1.3442220
X-RAY DIFFRACTIONf_chiral_restr0.08243
X-RAY DIFFRACTIONf_plane_restr0.009290
X-RAY DIFFRACTIONf_dihedral_angle_d15.164581
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.191-1.2190.2111140.1663737385185
1.219-1.2490.1521180.11944044522100
1.249-1.2830.1281330.10543764509100
1.283-1.3210.1471580.10144064564100
1.321-1.3630.1151350.09843474482100
1.363-1.4120.1111290.09344354564100
1.412-1.4690.1261460.09343684514100
1.469-1.5360.131420.09444364578100
1.536-1.6160.1241350.09644284563100
1.616-1.7180.1151250.10444284553100
1.718-1.850.1351360.11544674603100
1.85-2.0360.1151550.1244364591100
2.036-2.330.1381480.13244734621100
2.33-2.9340.2011480.16445294677100
2.934-19.5540.1831450.15947344879100

+
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