4NOT | pdb_00004not

Crystal structure of Dioclea sclerocarpa lectin complexed with X-man

• PDB DOI: https://doi.org/10.2210/pdb4NOT/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Macropsychanthus sclerocarpus
• Mutation(s): No 


• Deposited: 2013-11-20 Released: 2015-01-21 
• Deposition Author(s): Barroso-Neto, I.L., Teixeira, C.S., Correia, J.L.A., Santiago, M.Q., Pinto-Junior, V.R., Osterne, V.J.S., Plinio, D., Rocha, B.A.M., Cavada, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.257 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal structure of Dioclea sclerocarpa lectin complexed with X-man

Barroso-Neto, I.L., Teixeira, C.S., Correia, J.L.A., Santiago, M.Q., Pinto-Junior, V.R., Osterne, V.J.S., Plinio, D., Rocha, B.A.M., Cavada, B.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: 26.14 kDa 
• Atom Count: 1,905 
• Modeled Residue Count: 234 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin alpha chain	A	237	Macropsychanthus sclerocarpus	Mutation(s): 0
UniProt
Find proteins for B3EWJ2 (Macropsychanthus sclerocarpus) Explore B3EWJ2  Go to UniProtKB:  B3EWJ2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XMM	D [auth A]	5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside C14 H15 Br Cl N O6 OPIFSICVWOWJMJ-HAAGFXOZSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.257 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.94	α = 90
b = 66.61	β = 90
c = 108.65	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-21 
Deposition Author(s): Barroso-Neto, I.L., Teixeira, C.S., Correia, J.L.A., Santiago, M.Q., Pinto-Junior, V.R., Osterne, V.J.S., Plinio, D., Rocha, B.A.M., Cavada, B.S.

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Structure summary