5IIC

Crystal structure of red abalone VERL repeat 3 at 2.9 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5IIC/pdb

• Classification: CELL ADHESION
• Organism(s): Escherichia coli K-12, Haliotis rufescens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2016-03-01 Released: 2017-06-14 
• Deposition Author(s): Sadat Al-Hosseini, H., Raj, I., Nishimura, K., Jovine, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.310 
• R-Value Work: 0.251 
• R-Value Observed: 0.255 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 110.67 kDa 
• Atom Count: 7,360 
• Modelled Residue Count: 939 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Vitelline envelope sperm lysin receptor	A, B	496	Escherichia coli K-12, Haliotis rufescens This entity is chimeric	Mutation(s): 13  Gene Names: malE, b4034, JW3994, VERL
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q8WR62 (Haliotis rufescens) Explore Q8WR62  Go to UniProtKB:  Q8WR62
UniProt Groups	P0AEX9Q8WR62

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth B], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C, D	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.310 
• R-Value Work: 0.251 
• R-Value Observed: 0.255 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.33	α = 90
b = 81.64	β = 99.6
c = 111.63	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Sadat Al-Hosseini, H., Raj, I., Nishimura, K., Jovine, L.

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2017-06-28
  Changes: Database references
• Version 1.2: 2017-11-29
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary