1D1K | pdb_00001d1k

MUTATED SHIGA-LIKE TOXIN B SUBUNIT (D17E/W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE

• PDB DOI: https://doi.org/10.2210/pdb1D1K/pdb

• Classification: TOXIN
• Organism(s): Phage h30
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.218 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.191 (DCC) 

Literature

Mutated Shiga-like toxin B subunit (D17E/W34A) complexed with receptor Gb3 analogue

Ling, H., 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: 40.51 kDa 
• Atom Count: 3,076 
• Modeled Residue Count: 345 
• Deposited Residue Count: 345 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SHIGA-LIKE TOXIN I SUBUNIT B	A, B, C, D, E	69	Phage h30	Mutation(s): 2
UniProt
Find proteins for P69178 (Bacteriophage H30) Explore P69178  Go to UniProtKB:  P69178

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	F, G, H, I, J	3		N/A
Glycosylation Resources
GlyTouCan: G79094AA GlyCosmos: G79094AA GlyGen: G79094AA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.218 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.191 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.223	α = 106.05
b = 44.131	β = 106.38
c = 53.71	γ = 99.26

Software Package:

Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-09-20 
Deposition Author(s): Ling, H., 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: 2012-07-18
  Changes: Source and taxonomy
• Version 1.4: 2017-10-04
  Changes: Refinement description
• Version 1.5: 2018-03-14
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary