4IYE | pdb_00004iye

Crystal structure of AdTx1 (rho-Da1a) from eastern green mamba (Dendroaspis angusticeps)

• PDB DOI: https://doi.org/10.2210/pdb4IYE/pdb

• Classification: TOXIN
• Organism(s): Dendroaspis angusticeps
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-01-28 Released: 2013-05-08 
• Deposition Author(s): Stura, E.A., Vera, L., Maiga, A.A., Marchetti, C., Lorphelin, A., Bellanger, L., Servant, D., Gilles, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.252 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Crystallization of recombinant green mamba rho-Da1a toxin during a lyophilization procedure and its structure determination.

Maiga, A., Vera, L., Marchetti, C., Lorphelin, A., Bellanger, L., Mourier, G., Servent, D., Gilles, N., Stura, E.A.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 704-709

• PubMed: 23722859 
• DOI: https://doi.org/10.1107/S1744309113011470
• Primary Citation Related Structures: 
  4IYE


• PubMed Abstract: 
  

  ρ-Da1a toxin from eastern green mamba (Dendroaspis angusticeps) venom is a polypeptide of 65 amino acids with a strong affinity for the G-protein-coupled α(1A)-adrenoceptor. This neurotoxin has been crystallized from resolubilized lyophilized powder, but the best crystals grew spontaneously during lyophilization. The crystals belonged to the trigonal space group P3(1)21, with unit-cell parameters a = b = 37.37, c = 66.05 Å, and diffracted to 1.95 Å resolution. The structure solved by molecular replacement showed strong similarities to green mamba muscarinic toxins.

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Organizational Affiliation: 
• CEA, DSV, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.57 kDa 
• Atom Count: 598 
• Modeled Residue Count: 66 
• Deposited Residue Count: 66 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin AdTx1	A	66	Dendroaspis angusticeps	Mutation(s): 1
UniProt
Find proteins for P85092 (Dendroaspis angusticeps) Explore P85092  Go to UniProtKB:  P85092

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A], D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.252 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.37	α = 90
b = 37.37	β = 90
c = 66.05	γ = 120

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Stura, E.A., Vera, L., Maiga, A.A., Marchetti, C., Lorphelin, A., Bellanger, L., Servant, D., Gilles, N.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2013-08-28
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary