7AXY | pdb_00007axy

Crystal structure of a shortened IpgC variant in complex with 3-amino-5-(pyrrolidin-1-yl)-1H-pyrazole-4-carbonitrile

• PDB DOI: https://doi.org/10.2210/pdb7AXY/pdb

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


• Deposited: 2020-11-10 Released: 2021-11-24 
• Deposition Author(s): Gardonyi, M., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a shortened IpgC variant in complex with 3-amino-5-(pyrrolidin-1-yl)-1H-pyrazole-4-carbonitrile

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: 32.97 kDa 
• Atom Count: 2,292 
• Modeled Residue Count: 263 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E9Q	G [auth B]	5-azanyl-3-pyrrolidin-1-yl-1~{H}-pyrazole-4-carbonitrile C8 H11 N5 RQDSNKYYHIZWJX-UHFFFAOYSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.517	α = 90
b = 57.517	β = 90
c = 159.445	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Gardonyi, M., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description