4R7J | pdb_00004r7j

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase with the Internal Deletion Containing CBS Domain from Campylobacter jejuni

• PDB DOI: https://doi.org/10.2210/pdb4R7J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-08-27 Released: 2014-09-17 
• Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Hedstrom, L., Anderson, W.F., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Inosine 5'-monophosphate Dehydrogenase with the Internal Deletion Containing CBS Domain from Campylobacter jejuni

Kim, Y., Makowska-Grzyska, M., Gu, M., Hedstrom, L., Anderson, W.F., Joachimiak, A., 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)

Macromolecule Content 

• Total Structure Weight: 41.97 kDa 
• Atom Count: 2,853 
• Modeled Residue Count: 357 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A	385	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0  Gene Names: guaB, Cj1058c EC: 1.1.1.205
UniProt
Find proteins for Q0P9J4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0P9J4  Go to UniProtKB:  Q0P9J4

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMP	B [auth A]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N
MPD	H [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34r7j

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.413	α = 90
b = 119.413	β = 90
c = 69.394	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: 2014-09-17 
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Hedstrom, L., Anderson, W.F., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2017-02-08
  Changes: Database references, Structure summary
• Version 1.2: 2017-08-02
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description