4MYE | pdb_00004mye

Cymosema roseum seed lectin structure complexed with X-man

• PDB DOI: https://doi.org/10.2210/pdb4MYE/pdb

• Classification: Carbohydrate-binding protein
• Organism(s): Cymbosema roseum
• Mutation(s): No 


• Deposited: 2013-09-27 Released: 2014-10-01 
• Deposition Author(s): Barroso-Neto, I.L., Rocha, B.A.M., Teixeira, C.S., Santiago, M.Q., Souza, L.A.G., Pires, A.F., Assreuy, A.M.S., Delatorre, P., Cavada, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Cymosema roseum seed lectin structure complexed with X-man

Barroso-Neto, I.L., Rocha, B.A.M., Teixeira, C.S., Santiago, M.Q., Souza, L.A.G., Pires, A.F., Assreuy, A.M.S., Delatorre, P., Cavada, B.S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 25.84 kDa 
• Atom Count: 2,078 
• Modeled Residue Count: 237 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cymbosema roseum mannose-specific lectin	A	237	Cymbosema roseum	Mutation(s): 0
UniProt
Find proteins for P86184 (Cymbosema roseum) Explore P86184  Go to UniProtKB:  P86184

Small Molecules

Ligands 4 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
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.365	α = 90
b = 88.753	β = 90
c = 90.626	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	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: 2014-10-01 
Deposition Author(s): Barroso-Neto, I.L., Rocha, B.A.M., Teixeira, C.S., Santiago, M.Q., Souza, L.A.G., Pires, A.F., Assreuy, A.M.S., Delatorre, P., Cavada, B.S.

Revision History  

• Version 1.0: 2014-10-01
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 1.4: 2024-02-28
  Changes: Data collection, Database references, Structure summary