1OMY | pdb_00001omy

Crystal Structure of a Recombinant alpha-insect Toxin BmKaIT1 from the scorpion Buthus martensii Karsch

• PDB DOI: https://doi.org/10.2210/pdb1OMY/pdb

• Classification: TOXIN
• Organism(s): Olivierus martensii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2003-02-26 Released: 2003-09-09 
• Deposition Author(s): Huang, Y., Huang, Q., Chen, H., Tang, Y., Miyake, H., Kusunoki, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.218 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystallization and preliminary crystallographic study of rBmKalphaIT1, a recombinant alpha-insect toxin from the scorpion Buthus martensii Karsch.

Huang, Y., Huang, Q., Chen, H., Tang, Y., Miyake, H., Kusunoki, M.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1635-1636

• PubMed: 12925796 
• DOI: https://doi.org/10.1107/s090744490301415x
• Primary Citation Related Structures: 
  1OMY


• PubMed Abstract: 
  

  Alpha-insect scorpion toxins are a distinct group of scorpion neurotoxins for which no crystal structures are yet available. A novel alpha-insect toxin named BmKalphaIT1 from the scorpion Buthus martensii Karsch (BmK) has been expressed as an inclusion body in Escherichia coli and purified by chromatography after renaturation. Recombinant BmKalphaIT1 (rBmKaIT1) was crystallized using the vapour-diffusion technique in hanging drops at 296 K. The crystals, which were grown in sodium phosphate, belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 30.24 (1), b = 36.51 (3), c = 57.08 (2) A. Diffraction data were collected to 2.1 A resolution using synchrotron radiation. There appears to be one rBmKalphaIT1 molecule in the asymmetric unit.

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Organizational Affiliation: 
• Department of Chemical Biology, College of Chemistry, Peking University, Beijing 100871, People's Republic of China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.43 kDa 
• Atom Count: 542 
• Modeled Residue Count: 64 
• Deposited Residue Count: 65 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-neurotoxin TX12	A	65	Olivierus martensii	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q9GQW3 (Olivierus martensii) Explore Q9GQW3  Go to UniProtKB:  Q9GQW3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.218 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.241	α = 90
b = 36.507	β = 90
c = 57.08	γ = 90

Software Package:

Software Name	Purpose
DPS	data collection
DPS	data reduction
CNS	refinement
MOSFLM	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-09 
Deposition Author(s): Huang, Y., Huang, Q., Chen, H., Tang, Y., Miyake, H., Kusunoki, M.

Revision History  

• Version 1.0: 2003-09-09
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.4: 2023-11-08
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary