5AZA

Crystal structure of MBP-sAglB fusion protein with a 20-residue spacer in the connector helix

• PDB DOI: https://doi.org/10.2210/pdb5AZA/pdb

• Classification: SUGAR BINDING PROTEIN, TRANSFERASE
• Organism(s): Escherichia coli K-12, Pyrococcus furiosus COM1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-09-27 Released: 2016-01-13 
• Deposition Author(s): Matsuoka, R., Kohda, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.248 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 97.5 kDa 
• Atom Count: 6,733 
• Modelled Residue Count: 836 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Oligosaccharyl transferase stt3 subunit related protein	A	872	Escherichia coli K-12, Pyrococcus furiosus COM1 This entity is chimeric	Mutation(s): 1  Gene Names: malE, b4034, JW3994, PFC_07420
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for I6V0B8 (Pyrococcus furiosus COM1) Explore I6V0B8  Go to UniProtKB:  I6V0B8
UniProt Groups	I6V0B8P0AEX9

Oligosaccharides

Help

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.248 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.468	α = 90
b = 100.467	β = 90
c = 140.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Matsuoka, R., Kohda, D.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Data collection, Database references, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary