4FXS | pdb_00004fxs

Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae complexed with IMP and mycophenolic acid

• PDB DOI: https://doi.org/10.2210/pdb4FXS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-03 Released: 2012-07-25 
• Deposition Author(s): Osipiuk, J., Maltseva, N., Makowska-Grzyska, M., Jedrzejczak, R., 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: 2.24 Å
• R-Value Free: 
  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae complexed with IMP and mycophenolic acid.

Osipiuk, J., Maltseva, N., Makowska-Grzyska, M., Jedrzejczak, R., 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: 54.32 kDa 
• Atom Count: 3,667 
• Modeled Residue Count: 467 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A	496	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC0767, VC_0767 EC: 1.1.1.205
UniProt
Find proteins for Q9KTW3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KTW3  Go to UniProtKB:  Q9KTW3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMP	B [auth A]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N
MOA	C [auth A]	MYCOPHENOLIC ACID C17 H20 O6 HPNSFSBZBAHARI-RUDMXATFSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34fxs

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.96	α = 90
b = 111.96	β = 90
c = 188.994	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-25 
Deposition Author(s): Osipiuk, J., Maltseva, N., Makowska-Grzyska, M., Jedrzejczak, R., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-07-25
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary