5VXJ

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.259
R-Value Work: 0.196
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18013
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.259
R-Value Work: 0.196
R-Value Observed: 0.200
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-08-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-08-30
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.