[English] 日本語
Yorodumi
- PDB-8g0f: Crystal structure of diphtheria toxin H223Q/H257Q double mutant (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8g0f
TitleCrystal structure of diphtheria toxin H223Q/H257Q double mutant (pH 5.5)
ComponentsDiphtheria toxin
KeywordsTOXIN / diptheria toxin / pH dependent conformational changes
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase activity / toxin activity / extracellular space
Similarity search - Function
Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain superfamily / Diphtheria toxin, R domain / Diphtheria toxin (NAD+-dipthamide ADP-ribosyltransferase) / Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain
Similarity search - Domain/homology
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Ladokhin, A.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: Toxins / Year: 2023
Title: Histidine Protonation and Conformational Switching in Diphtheria Toxin Translocation Domain.
Authors: Rodnin, M.V. / Vasques-Montes, V. / Kyrychenko, A. / Oliveira, N.F.B. / Kashipathy, M.M. / Battaile, K.P. / Douglas, J. / Lovell, S. / Machuqueiro, M. / Ladokhin, A.S.
History
DepositionJan 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diphtheria toxin
B: Diphtheria toxin


Theoretical massNumber of molelcules
Total (without water)117,4502
Polymers117,4502
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-29 kcal/mol
Surface area40340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.548, 69.471, 72.879
Angle α, β, γ (deg.)117.99, 93.87, 99.34
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Diphtheria toxin


Mass: 58724.797 Da / Num. of mol.: 2 / Mutation: K51E, E148K, H223Q, H257Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL23DELysS / References: UniProt: Q5PY51
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% (w/v) PEG 2000 MME, 100 mM sodium citrate tribasic, 200 mM sodium malonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→46.78 Å / Num. obs: 52984 / % possible obs: 95.8 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.047 / Rrim(I) all: 0.088 / Χ2: 0.92 / Net I/σ(I): 9.7 / Num. measured all: 182683
Reflection shellResolution: 2.25→2.32 Å / % possible obs: 96.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.727 / Num. measured all: 15664 / Num. unique obs: 4660 / CC1/2: 0.692 / Rpim(I) all: 0.469 / Rrim(I) all: 0.869 / Χ2: 0.81 / Net I/σ(I) obs: 1.7

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→36.31 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 2608 4.92 %
Rwork0.1904 --
obs0.1937 52961 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→36.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7506 0 0 167 7673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017654
X-RAY DIFFRACTIONf_angle_d0.96910419
X-RAY DIFFRACTIONf_dihedral_angle_d14.4912649
X-RAY DIFFRACTIONf_chiral_restr0.0521222
X-RAY DIFFRACTIONf_plane_restr0.0071343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30.32111210.27532700X-RAY DIFFRACTION96
2.3-2.340.34071400.2462701X-RAY DIFFRACTION97
2.34-2.390.2631470.24912655X-RAY DIFFRACTION97
2.39-2.440.29581140.24422708X-RAY DIFFRACTION97
2.44-2.50.32731170.24752739X-RAY DIFFRACTION98
2.5-2.560.35351660.25772660X-RAY DIFFRACTION97
2.56-2.630.30471360.24082724X-RAY DIFFRACTION98
2.63-2.70.33611280.2452238X-RAY DIFFRACTION81
2.71-2.790.33331450.22732738X-RAY DIFFRACTION98
2.79-2.890.30281200.2342733X-RAY DIFFRACTION98
2.89-3.010.33031360.2372686X-RAY DIFFRACTION98
3.01-3.140.31221530.23942706X-RAY DIFFRACTION98
3.14-3.310.30871520.21262719X-RAY DIFFRACTION98
3.31-3.520.26351110.19562301X-RAY DIFFRACTION84
3.52-3.790.24171700.17412648X-RAY DIFFRACTION97
3.79-4.170.21381490.15292669X-RAY DIFFRACTION97
4.17-4.770.1791360.12922690X-RAY DIFFRACTION97
4.77-6.010.21861740.15862630X-RAY DIFFRACTION96
6.01-36.310.2156930.16862708X-RAY DIFFRACTION96

+
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