6MGR | pdb_00006mgr

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with inhibitor Oxanosine monophosphate

• PDB DOI: https://doi.org/10.2210/pdb6MGR/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Campylobacter jejuni
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-09-14 Released: 2018-10-24 
• Deposition Author(s): Kim, Y., Maltseva, N., Yu, R., Hedstrom, L., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Campylobacter jejuni in the complex with inhibitor Oxanosine Monophosphate

Kim, Y., Maltseva, N., Yu, R., Hedstrom, L., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 168.22 kDa 
• Atom Count: 11,602 
• Modeled Residue Count: 1,449 
• Deposited Residue Count: 1,540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine monophosphate dehydrogenase	A, B, C, D	385	Campylobacter jejuni	Mutation(s): 0  Gene Names: C9J79_08320 EC: 1.1.1.205

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JQS	E [auth A], IA [auth D], O [auth B], Z [auth C]	5-[(Z)-(aminomethylidene)amino]-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole-4-carboxylic acid C10 H15 N4 O9 P CEVAZLJDKSQTJT-FJGDRVTGSA-N
MPD	GA [auth C], L [auth A], X [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	AA [auth C], CA [auth C], DA [auth C], EA [auth C], F [auth A], FA [auth C], G [auth A], JA [auth D], KA [auth D], LA [auth D], P [auth B], Q [auth B], QA [auth D], R [auth B], S [auth B], T [auth B], V [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
K	HA [auth D], M [auth A], N [auth B], U [auth B], Y [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	BA [auth C], H [auth A], I [auth A], J [auth A], K [auth A], MA [auth D], NA [auth D], OA [auth D], PA [auth D], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.343	α = 90
b = 119.592	β = 89.99
c = 119.307	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Kim, Y., Maltseva, N., Yu, R., Hedstrom, L., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description