3NBC

Clitocybe nebularis ricin B-like lectin (CNL) in complex with lactose, crystallized at pH 4.4

• PDB DOI: https://doi.org/10.2210/pdb3NBC/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Clitocybe nebularis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-03 Released: 2011-09-21 
• Deposition Author(s): Renko, M., Pohleven, J., Sabotic, J., Kos, J., Turk, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.01 Å
• R-Value Free: 0.172 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 

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: 32.08 kDa 
• Atom Count: 2,936 
• Modelled Residue Count: 296 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin B-like lectin	A, B	148	Clitocybe nebularis	Mutation(s): 0
UniProt
Find proteins for B2ZRS9 (Clitocybe nebularis) Explore B2ZRS9  Go to UniProtKB:  B2ZRS9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G84224TW GlyCosmos:  G84224TW GlyGen:  G84224TW

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	C	beta-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.01 Å
• R-Value Free: 0.172 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.789	α = 90
b = 55.898	β = 90
c = 112.414	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Renko, M., Pohleven, J., Sabotic, J., Kos, J., Turk, D.

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2012-03-07
  Changes: Database references
• Version 1.2: 2014-03-19
  Changes: Database references
• Version 1.3: 2017-11-08
  Changes: Advisory, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-03-20
  Changes: Advisory, Data collection, Database references, Structure summary
• Version 2.2: 2024-04-03
  Changes: Refinement description