4IYB | pdb_00004iyb

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

• PDB DOI: https://doi.org/10.2210/pdb4IYB/pdb

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


• Deposited: 2013-01-28 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: 1.59 Å
• R-Value Free: 
  0.163 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

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

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.15 kDa 
• Atom Count: 2,715 
• Modeled Residue Count: 280 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAL	C [auth A]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
GOL	D [auth A], E [auth A], F [auth B], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.163 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.596	α = 90
b = 63.596	β = 90
c = 155.831	γ = 120

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 1.1: 2017-11-15
  Changes: Advisory, Refinement description
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-09-20
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary