4Q32

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and C91

• PDB DOI: https://doi.org/10.2210/pdb4Q32/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridium perfringens ATCC 13124
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-04-10 Released: 2014-07-09 
• Deposition Author(s): Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Gu, M., Zhang, M., Mandapati, K., Gollapalli, D.R., Gorla, S.K., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.223 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 

Starting Model: experimental

Literature

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase from Clostridium perfringens Complexed with IMP and C91

Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Gu, M., Zhang, M., Mandapati, K., Gollapalli, D.R., Gorla, S.K., Hedstrom, L., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 156.67 kDa 
• Atom Count: 10,326 
• Modelled Residue Count: 1,358 
• Deposited Residue Count: 1,452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B, C, D	363	Clostridium perfringens ATCC 13124	Mutation(s): 0  Gene Names: CPF_2558, guaB EC: 1.1.1.205
UniProt
Find proteins for A0A0H2YRZ7 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YRZ7  Go to UniProtKB:  A0A0H2YRZ7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C91	F [auth A], G [auth A], I [auth B], K [auth D]	N-(naphthalen-2-yl)-2-[2-(pyridin-2-yl)-1H-benzimidazol-1-yl]acetamide C24 H18 N4 O XYCMWFINXXFAFG-UHFFFAOYSA-N
IMP	E [auth A], H [auth B], J [auth C], L [auth D]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.223 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 
• Space Group: P 4₃
• Diffraction Data: https://doi.org/10.18430/m34q32

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.611	α = 90
b = 77.611	β = 90
c = 222.726	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Maltseva, N., Kim, Y., Makowska-Grzyska, M., Mulligan, R., Gu, M., Zhang, M., Mandapati, K., Gollapalli, D.R., Gorla, S.K., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2017-07-26
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description