3ZXC | pdb_00003zxc

E69 deletion mutant single insulin-like growth factor binding domain protein (SIBD-1) from Cupiennius salei

• PDB DOI: https://doi.org/10.2210/pdb3ZXC/pdb

• Classification: SIGNALING
• Organism(s): Cupiennius salei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-09 Released: 2012-06-06 
• Deposition Author(s): Widmer, C., Baumann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.191 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Structural and Biochemical Characterization of Native and Recombinant Single Insulin-Like Growth Factor-Binding Domain Protein (Sibd-1) from the Central American Hunting Spider Cupiennius Salei (Ctenidae).

Trachsel, C., Widmer, C., Kampfer, U., Buhr, C., Baumann, T., Kuhn-Nentwig, L., Schurch, S., Schaller, J., Baumann, U.

(2012) Proteins 80: 2323

• PubMed: 22622866 
• DOI: https://doi.org/10.1002/prot.24119


• PubMed Abstract: 
  

  Cupiennius salei single insulin-like growth factor binding domain protein (SIBD-1) is an 8.6 kDa Cys-, Pro-, and Gly-rich protein, discovered in the hemocytes of the Central American hunting spider Cupiennius salei. SIBD-1 exhibits high sequence similarity to the N-terminal domain of the insulin-like growth factor-binding protein superfamily and has been reported to play an important role in the spider's immune system. Here, the recombinant expression and the elucidation of the three-dimensional structure of recombinant SIBD-1 and the characterization of the sugar moiety at Thr2 of native SIBD-1 is described in detail.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 16.19 kDa 
• Atom Count: 1,286 
• Modeled Residue Count: 145 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SINGLE INSULIN-LIKE GROWTH FACTOR-BINDING DOMAIN PROTEIN-1	A, B	77	Cupiennius salei	Mutation(s): 0
UniProt
Find proteins for G4V4F9 (Cupiennius salei) Explore G4V4F9  Go to UniProtKB:  G4V4F9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.191 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.46	α = 90
b = 49.46	β = 90
c = 121.499	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHELXCD	phasing
SHELXE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Widmer, C., Baumann, U.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2012-08-08
  Changes: Database references
• Version 2.0: 2024-11-20
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary