[English] 日本語
Yorodumi
- PDB-1sgk: NUCLEOTIDE-FREE DIPHTHERIA TOXIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sgk
TitleNUCLEOTIDE-FREE DIPHTHERIA TOXIN
ComponentsDIPHTHERIA TOXIN (DIMERIC)
KeywordsTOXIN / ADP-RIBOSYLATION / TRANSFERASE / GLYCOSYLTRANSFERASE / NAD / ADP-RIBOSYL TRANSFERASE
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / Uptake and function of diphtheria toxin / protein transmembrane transporter activity / nucleotidyltransferase activity / toxin activity / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Diphtheria toxin, translocation domain / Diphtheria toxin, receptor-binding domain / 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 ...Diphtheria toxin, translocation domain / Diphtheria toxin, receptor-binding domain / 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 / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Globin-like / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesCorynephage beta (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBell, C.E. / Eisenberg, D.
Citation
Journal: Biochemistry / Year: 1997
Title: Crystal structure of nucleotide-free diphtheria toxin.
Authors: Bell, C.E. / Eisenberg, D.
#1: Journal: Biochemistry / Year: 1996
Title: Crystal Structure of Diphtheria Toxin Bound to Nicotinamide Adenine Dinucleotide
Authors: Bell, C.E. / Eisenberg, D.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Domain Swapping: Entangling Alliances between Proteins
Authors: Bennett, M.J. / Choe, S. / Eisenberg, D.
#3: Journal: Protein Sci. / Year: 1994
Title: Refined Structure of Monomeric Diphtheria Toxin at 2.3 A Resolution
Authors: Bennett, M.J. / Eisenberg, D.
#4: Journal: Protein Sci. / Year: 1994
Title: Refined Structure of Dimeric Diphtheria Toxin at 2.0 A Resolution
Authors: Bennett, M.J. / Choe, S. / Eisenberg, D.
#5: Journal: Nature / Year: 1992
Title: The Crystal Structure of Diphtheria Toxin
Authors: Choe, S. / Bennett, M.J. / Fujii, G. / Curmi, P.M. / Kantardjieff, K.A. / Collier, R.J. / Eisenberg, D.
History
DepositionSep 12, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIPHTHERIA TOXIN (DIMERIC)


Theoretical massNumber of molelcules
Total (without water)58,4111
Polymers58,4111
Non-polymers00
Water6,431357
1
A: DIPHTHERIA TOXIN (DIMERIC)

A: DIPHTHERIA TOXIN (DIMERIC)


Theoretical massNumber of molelcules
Total (without water)116,8232
Polymers116,8232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area8350 Å2
ΔGint-26 kcal/mol
Surface area41190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.200, 91.200, 65.300
Angle α, β, γ (deg.)90.00, 94.20, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein DIPHTHERIA TOXIN (DIMERIC) / DT


Mass: 58411.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURCHASED FROM CONNAUGHT LABORATORIES / Source: (natural) Corynephage beta (virus) / Genus: Lambda-like viruses
References: UniProt: P00588, NAD+-diphthamide ADP-ribosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.67 Å3/Da / Density % sol: 46 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP, 12 % PEG8000, 0.43M NACL, 0.043M TRIS, PH 7.5, vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %(w/v)PEG80001reservoir
20.43 M1reservoirNaCl
30.043 MTris1reservoir
425 mg/mlDT1drop
514 %(w/v)PEG80001drop
60.5 M1dropNaCl
70.05 MTris1drop

-
Data collection

DiffractionMean temperature: 94 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 15, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 26627 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.6
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 2.6 / % possible all: 92.7
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. measured all: 74281
Reflection shell
*PLUS
% possible obs: 92.7 %

-
Processing

Software
NameVersionClassification
R-AXISdata collection
R-AXISdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DT-DIMER APUP COMPLEX (PDB ENTRY 1DDT)

1ddt


Resolution: 2.3→8 Å / Cross valid method: FREE R-FACTOR / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2565 10 %RANDOM
Rwork0.182 ---
obs0.182 25726 96.2 %-
Displacement parametersBiso mean: 38.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4021 0 0 357 4378
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.3→2.4 Å
RfactorNum. reflection% reflection
Rfree0.351 325 81.5 %
Rwork0.2874 2729 -
obs--9.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 23161
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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://pdbjlvh1.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