2GDF | pdb_00002gdf

Crystal structure of Dioclea violacea seed lectin

• PDB DOI: https://doi.org/10.2210/pdb2GDF/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Macropsychanthus violaceus
• Mutation(s): No 


• Deposited: 2006-03-16 Released: 2006-09-16 
• Deposition Author(s): Gallego del Sol, F., Chornet, J.J.C., Cavada, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Crystal structure of Dioclea violacea seed lectin

Gallego del Sol, F., Chornet, J.J.C., Cavada, B.S.

To be published.

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: 102.55 kDa 
• Atom Count: 7,229 
• Modeled Residue Count: 926 
• Deposited Residue Count: 948 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lectin	A, B, C, D	237	Macropsychanthus violaceus	Mutation(s): 0
UniProt
Find proteins for P08902 (Dioclea grandiflora) Explore P08902  Go to UniProtKB:  P08902

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	E [auth B], G [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	F [auth B], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.938	α = 90
b = 72.938	β = 90
c = 161.362	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-16 
Deposition Author(s): Gallego del Sol, F., Chornet, J.J.C., Cavada, B.S.

Revision History  

• Version 1.0: 2006-09-16
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations