4WV8

Crystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with lactose

• PDB DOI: https://doi.org/10.2210/pdb4WV8/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Vatairea macrocarpa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-04 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: 1.83 Å
• R-Value Free: 0.195 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

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: 107.16 kDa 
• Atom Count: 8,314 
• Modelled Residue Count: 950 
• Deposited Residue Count: 964 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Seed lectin	A, B, C, D	241	Vatairea macrocarpa	Mutation(s): 0
UniProt
Find proteins for P81371 (Vatairea macrocarpa) Explore P81371  Go to UniProtKB:  P81371

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G88362QR GlyCosmos:  G88362QR GlyGen:  G88362QR

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	J [auth A], L [auth B], N [auth C], P [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	I [auth A], K [auth B], M [auth C], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900008	E, F, G, H	alpha-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.195 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.644	α = 90
b = 97.427	β = 94.68
c = 78.667	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary