7PE0 | pdb_00007pe0

Crystal structure of IpgC in complex with J52

• PDB DOI: https://doi.org/10.2210/pdb7PE0/pdb

• Classification: CHAPERONE
• Organism(s): Shigella flexneri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-08-09 Released: 2022-08-24 
• Deposition Author(s): Gardonyi, M., Heine, A., Klebe, G.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of IpgC in complex with J52

Gardonyi, M., Heine, A., Klebe, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.9 kDa 
• Atom Count: 2,400 
• Modeled Residue Count: 270 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone protein IpgC	A, B	143	Shigella flexneri	Mutation(s): 0  Gene Names: ipgC, ippI, CP0129
UniProt
Find proteins for P0A2U4 (Shigella flexneri) Explore P0A2U4  Go to UniProtKB:  P0A2U4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
483	D [auth A]	2-(1H-imidazol-1-yl)-N-(trans-4-methylcyclohexyl)acetamide C12 H19 N3 O PKHDTDLLHJFDKS-XYPYZODXSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.642	α = 90
b = 57.642	β = 90
c = 159.612	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Gardonyi, M., Heine, A., Klebe, G.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description