4B9H

Cladosporium fulvum LysM effector Ecp6 in complex with a beta-1,4- linked N-acetyl-D-glucosamine tetramer: I3C heavy atom derivative

• PDB DOI: https://doi.org/10.2210/pdb4B9H/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Fulvia fulva
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2012-09-04 Released: 2013-07-17 
• Deposition Author(s): Saleem-Batcha, R., Sanchez-Vallet, A., Hansen, G., Thomma, B.P.H.J., Mesters, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.266 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 

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: 25.93 kDa 
• Atom Count: 1,555 
• Modelled Residue Count: 189 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXTRACELLULAR PROTEIN 6	A	228	Fulvia fulva	Mutation(s): 0
UniProt
Find proteins for B3VBK9 (Passalora fulva) Explore B3VBK9  Go to UniProtKB:  B3VBK9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose	C	4		N/A
Glycosylation Resources
GlyTouCan:  G93613RO GlyCosmos:  G93613RO GlyGen:  G93613RO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I3C	E [auth A]	5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid C8 H4 I3 N O4 JEZJSNULLBSYHV-UHFFFAOYSA-N
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.266 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.889	α = 90
b = 57.889	β = 90
c = 119.679	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-17 
Deposition Author(s): Saleem-Batcha, R., Sanchez-Vallet, A., Hansen, G., Thomma, B.P.H.J., Mesters, J.R.

Revision History  

• Version 1.0: 2013-07-17
  Type: Initial release
  
• Version 1.1: 2013-09-25
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary