1M7D

Crystal structure of a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide complexed with a trisaccharide

• PDB DOI: https://doi.org/10.2210/pdb1M7D/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-07-19 Released: 2003-07-22 
• Deposition Author(s): Vyas, N.K., Vyas, M.N., Chervenak, M.C., Johnson, M.A., Pinto, B.M., Bundle, D.R., Quiocho, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.279 
• R-Value Work: 0.216 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 47.78 kDa 
• Atom Count: 3,478 
• Modelled Residue Count: 435 
• Deposited Residue Count: 435 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of the monoclonal antibody Fab SYA/J6	A	215	Mus musculus	Mutation(s): 0
UniProt
Find proteins for A2NHM3 (Mus musculus) Explore A2NHM3  Go to UniProtKB:  A2NHM3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of the monoclonal antibody Fab SYA/J6	B	220	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01801 (Mus musculus) Explore P01801  Go to UniProtKB:  P01801

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-rhamnopyranose-(1-3)-alpha-L-Olivopyranose-(1-3)-methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside	C	3		N/A
Glycosylation Resources
GlyTouCan:  G80462MI GlyCosmos:  G80462MI

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.279 
• R-Value Work: 0.216 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71	α = 90
b = 71	β = 90
c = 198	γ = 90

Software Package:

Software Name	Purpose
Weissenberg	data collection
WEIS	data reduction
Protein	data reduction
MERLOT	phasing
CNS	refinement
WEISSENBERG	data reduction
WEIS	data scaling
PROTEIN	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-22 
Deposition Author(s): Vyas, N.K., Vyas, M.N., Chervenak, M.C., Johnson, M.A., Pinto, B.M., Bundle, D.R., Quiocho, F.A.

Revision History  

• Version 1.0: 2003-07-22
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary