1D1I | pdb_00001d1i

MUTATED SHIGA-LIKE TOXIN B SUBUNIT (W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE

• PDB DOI: https://doi.org/10.2210/pdb1D1I/pdb

• Classification: TOXIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-09-17 Released: 2000-09-20 
• Deposition Author(s): Ling, H., Boodhoo, A., Brunton, J.L., Read, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.211 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.170 (DCC) 

Literature

Mutated Shiga-like Toxin B Subunit (W34A) Complexed with Receptor Gb3 Analogue

Ling, H., Boodhoo, A., Brunton, J.L., Read, R.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Macromolecule Content 

• Total Structure Weight: 40.78 kDa 
• Atom Count: 3,044 
• Modeled Residue Count: 345 
• Deposited Residue Count: 345 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SHIGA TOXIN B-CHAIN	A, B, C, D, E	69	Escherichia coli	Mutation(s): 1
UniProt
Find proteins for P69179 (Enterobacteria phage H19B) Explore P69179  Go to UniProtKB:  P69179

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose	F	2		N/A
Glycosylation Resources
GlyTouCan:  G67988RO GlyCosmos:  G67988RO GlyGen:  G67988RO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	G, H, I, J, K	3		N/A
Glycosylation Resources
GlyTouCan:  G00059MO GlyCosmos:  G00059MO GlyGen:  G00059MO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.211 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.170 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.232	α = 106.04
b = 44.136	β = 106.37
c = 53.881	γ = 99.22

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-09-20 
Deposition Author(s): Ling, H., Boodhoo, A., Brunton, J.L., Read, R.J.

Revision History  

• Version 1.0: 2000-09-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-11-03
  Changes: Database references, Structure summary
• Version 2.2: 2024-10-16
  Changes: Data collection, Structure summary