4XXA

Crystal structure of a recombinant Vatairea macrocarpa seed lectin

• PDB DOI: https://doi.org/10.2210/pdb4XXA/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Vatairea macrocarpa
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-01-30 Released: 2016-01-27 
• Deposition Author(s): Sousa, B.L., Silva-Filho, J.C., Kumar, P., Lyskowski, A., Bezerra, G.A., Delatorre, P., Rocha, B.A.M., Cunha, R.M.S., Nagano, C.S., Gruber, K., Cavada, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Crystal structure of a recombinant Vatairea macrocarpa seed lectin

Sousa, B.L., Silva-Filho, J.C., Kumar, P., Lyskowski, A., Bezerra, G.A., Delatorre, P., Rocha, B.A.M., Cunha, R.M.S., Nagano, C.S., Gruber, K., Cavada, B.S.

(2016) Int J Biochem Cell Biol 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 55.84 kDa 
• Atom Count: 3,816 
• Modelled Residue Count: 468 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Seed lectin	A, B	250	Vatairea macrocarpa	Mutation(s): 0
UniProt
Find proteins for P81371 (Vatairea macrocarpa) Explore P81371  Go to UniProtKB:  P81371

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	F [auth A], J [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
GOL	E [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	D [auth A], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	C [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.083	α = 90
b = 96.083	β = 90
c = 85.099	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALA	data scaling
PHASER	phasing
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Sousa, B.L., Silva-Filho, J.C., Kumar, P., Lyskowski, A., Bezerra, G.A., Delatorre, P., Rocha, B.A.M., Cunha, R.M.S., Nagano, C.S., Gruber, K., Cavada, B.S.

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Data collection
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description