[English] 日本語
Yorodumi
- PDB-7k7b: Crystal structure of diphtheria toxin from crystals obtained at pH 5.0 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k7b
TitleCrystal structure of diphtheria toxin from crystals obtained at pH 5.0
ComponentsDiphtheria toxin
KeywordsTOXIN / diptheria toxin / pH dependent conformational changes
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / toxin activity / extracellular space / identical protein binding
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
Diphtheria toxin / Diphtheria toxin
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Rodnin, M.V. / Ladokhin, A.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-069783 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: Toxins / Year: 2020
Title: Structure of the Diphtheria Toxin at Acidic pH: Implications for the Conformational Switching of the Translocation Domain.
Authors: Rodnin, M.V. / Kashipathy, M.M. / Kyrychenko, A. / Battaile, K.P. / Lovell, S. / Ladokhin, A.S.
History
DepositionSep 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Diphtheria toxin
B: Diphtheria toxin


Theoretical massNumber of molelcules
Total (without water)117,4902
Polymers117,4902
Non-polymers00
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-30 kcal/mol
Surface area40140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.045, 69.162, 73.376
Angle α, β, γ (deg.)122.070, 93.650, 97.900
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Diphtheria toxin


Mass: 58744.828 Da / Num. of mol.: 2 / Fragment: Full Length / Mutation: K51E, E148K
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, UniProt: Q6NK15*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.47 Å3/Da / Density % sol: 50.2 % / Mosaicity: 0.26 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10% (w/v) PEG 10000, 0.1 M magnesium acetate, 0.1 M MES

-
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: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→49.59 Å / Num. obs: 68617 / % possible obs: 97.3 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10 / Num. measured all: 239575 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.05-2.13.50.7921557344000.6811.796.6
9.83-49.593.70.02823196250.99831.398.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.16 Å49.59 Å

-
Processing

Software
NameVersionClassification
PHENIXdev_4000refinement
XDSdata reduction
Aimless0.7.1data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DDT

1ddt


Resolution: 2.05→36.61 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 29.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 3424 4.99 %
Rwork0.197 65164 -
obs0.1996 68588 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.38 Å2 / Biso mean: 50.285 Å2 / Biso min: 21.3 Å2
Refinement stepCycle: final / Resolution: 2.05→36.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7444 0 0 321 7765
Biso mean---45.99 -
Num. residues----1004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097590
X-RAY DIFFRACTIONf_angle_d0.91510319
X-RAY DIFFRACTIONf_dihedral_angle_d5.8111043
X-RAY DIFFRACTIONf_chiral_restr0.0511201
X-RAY DIFFRACTIONf_plane_restr0.0081329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.080.35241320.29842712284496
2.08-2.110.3161420.27012680282296
2.11-2.140.35431410.26732689283097
2.14-2.180.29671290.25052712284197
2.18-2.220.30171350.252747288297
2.22-2.260.29721320.25372685281797
2.26-2.30.321550.24822744289997
2.3-2.350.31071520.24142643279597
2.35-2.40.28541640.23912698286297
2.4-2.450.37121510.23622720287198
2.45-2.510.25381500.22932699284998
2.51-2.580.31491430.22642730287397
2.58-2.660.27011540.21932773292798
2.66-2.740.24591350.21352711284698
2.74-2.840.26951470.21792704285197
2.84-2.960.29061350.22632764289998
2.96-3.090.3131560.21952687284398
3.09-3.250.26031540.22012770292498
3.25-3.460.27781350.19942747288298
3.46-3.720.25961450.18472674281997
3.72-4.10.21021180.16362713283196
4.1-4.690.20471510.142682283397
4.69-5.90.1631360.16322744288098
5.91-36.610.21541320.18342736286897

+
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