4TKC | pdb_00004tkc

Japanese Marasmius oreades lectin complexed with mannose

• PDB DOI: https://doi.org/10.2210/pdb4TKC/pdb

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


• Deposited: 2014-05-26 Released: 2015-06-03 
• Deposition Author(s): Noma, Y., Shimokawa, M., Maeganeku, C., Motoshima, H., Watanabe, K., Minami, Y., Yagi, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 
  0.207 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Structure of Japanese Marasmius oreades lectin complexed with mannose.

Noma, Y., Shimokawa, M., Maeganeku, C., Motoshima, H., Watanabe, K., Yagi, F., Minami, Y.

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: 13.57 kDa 
• Atom Count: 1,067 
• Modeled Residue Count: 118 
• Deposited Residue Count: 120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannose recognizing lectin	A	120	Marasmius oreades	Mutation(s): 0  Gene Names: Mlec1
UniProt
Find proteins for I7H471 (Marasmius oreades) Explore I7H471  Go to UniProtKB:  I7H471

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	D [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	B [auth A]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free:  0.207 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.42	α = 90
b = 58.42	β = 90
c = 57.732	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-03 
Deposition Author(s): Noma, Y., Shimokawa, M., Maeganeku, C., Motoshima, H., Watanabe, K., Minami, Y., Yagi, F.

Revision History  

• Version 1.0: 2015-06-03
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Refinement description, Structure summary
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Structure summary