5VXJ | pdb_00005vxj

2.50 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JMK-E3

• PDB DOI: https://doi.org/10.2210/pdb5VXJ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Shigella flexneri, Vicugna pacos
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-05-23 Released: 2017-08-30 
• Deposition Author(s): Barta, M.L., Lovell, S., Battaile, K.P., Picking, W.D., Picking, W.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

2.50 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JMK-E3

Barta, M.L., Lovell, S., Battaile, K.P., Picking, W.D., Picking, W.L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 237.84 kDa 
• Atom Count: 15,130 
• Modeled Residue Count: 1,955 
• Deposited Residue Count: 2,175 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Invasin IpaD	A, C, E, G, I	289	Shigella flexneri	Mutation(s): 1  Gene Names: ipaD, CP0126
UniProt
Find proteins for P18013 (Shigella flexneri) Explore P18013  Go to UniProtKB:  P18013

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
single-domain antibody JMK-E3	B, D, F, H, J	146	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.014	α = 90
b = 163.35	β = 90
c = 216.021	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Barta, M.L., Lovell, S., Battaile, K.P., Picking, W.D., Picking, W.L.

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary