4J2S | pdb_00004j2s

Macrolepiota procera ricin B-like lectin (MPL) in complex with Di-LacNAc

• PDB DOI: https://doi.org/10.2210/pdb4J2S/pdb

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


• Deposited: 2013-02-05 Released: 2013-11-20 
• Deposition Author(s): Renko, M., Zurga, S., Sabotic, J., Pohleven, J., Kos, J., Turk, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.175 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Macrolepiota procera ricin B-like lectin (MPL) in complex with Di-LacNAc

Renko, M., Zurga, S., Sabotic, J., Pohleven, J., Kos, J., Turk, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.32 kDa 
• Atom Count: 1,377 
• Modeled Residue Count: 139 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin B-like lectin	A	140	Macrolepiota procera	Mutation(s): 0
UniProt
Find proteins for F6KMV5 (Macrolepiota procera) Explore F6KMV5  Go to UniProtKB:  F6KMV5

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside	B	2		N/A
Glycosylation Resources
GlyTouCan: G74782FX GlyCosmos: G74782FX

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN	C [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.175 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.737	α = 90
b = 56.458	β = 90
c = 61.279	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
MAIN	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-20 
Deposition Author(s): Renko, M., Zurga, S., Sabotic, J., Pohleven, J., Kos, J., Turk, D.

Revision History  

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.0: 2021-08-04
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description