4H3O | pdb_00004h3o

Crystal structure of a new form of lectin from Allium sativum at 2.17 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4H3O/pdb

• Classification: PLANT PROTEIN
• Organism(s): Allium sativum
• Mutation(s): No 


• Deposited: 2012-09-14 Released: 2012-09-26 
• Deposition Author(s): Kumar, S., Yamini, S., Kumar, J., Kaur, P., Singh, T.P., Dey, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a new form of lectin from Allium sativum at 2.17 A resolution

Kumar, S., Yamini, S., Kumar, J., Kaur, P., Singh, T.P., Dey, S.

To be published.

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: 23.82 kDa 
• Atom Count: 1,823 
• Modeled Residue Count: 210 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A, B	105	Allium sativum	Mutation(s): 0
UniProt
Find proteins for K4DIE9 (Allium sativum) Explore K4DIE9  Go to UniProtKB:  K4DIE9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
NA	J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.513	α = 90
b = 57.234	β = 90
c = 97.449	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-26 
Deposition Author(s): Kumar, S., Yamini, S., Kumar, J., Kaur, P., Singh, T.P., Dey, S.

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary