1C4Q | pdb_00001c4q

MUTATED SHIGA-LIKE TOXIN B SUBUNIT (F30A/W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE

• PDB DOI: https://doi.org/10.2210/pdb1C4Q/pdb

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


• Deposited: 1999-08-31 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: 1.52 Å
• R-Value Free: 
  0.194 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Identification of the Primary Receptor Binding Site of Shiga-Like Toxin B Subunits: Structures of Mutated Shiga-Like Toxin I B-Pentamer with and without Bound Carbohydrate

Ling, H., Bast, D., 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: 40.06 kDa 
• Atom Count: 3,232 
• Modeled Residue Count: 345 
• Deposited Residue Count: 345 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)	A, B, C, D, E	69	Escherichia coli	Mutation(s): 2
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-(1-4)-beta-D-glucopyranose	F, G, H, I, J	3		N/A
Glycosylation Resources
GlyTouCan:  G00059MO GlyCosmos:  G00059MO GlyGen:  G00059MO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.194 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.269	α = 106.24
b = 44.165	β = 106.69
c = 54.007	γ = 98.87

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: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-03-07
  Changes: Data collection
• Version 1.5: 2018-03-14
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-08-09
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary