4XTM | pdb_00004xtm

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

• PDB DOI: https://doi.org/10.2210/pdb4XTM/pdb

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


• Deposited: 2015-01-23 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: 2.70 Å
• R-Value Free: 
  0.244 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.207 (Depositor) 

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: 28.19 kDa 
• Atom Count: 1,891 
• Modeled Residue Count: 233 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2G	D [auth A]	2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N
CIT	E [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.244 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.354	α = 90
b = 86.111	β = 90
c = 129.023	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-02-28
  Changes: Data collection, Database references, Structure summary