4IBO | pdb_00004ibo

Crystal structure of a putative gluconate dehydrogenase from agrobacterium tumefaciens (target EFI-506446)

• PDB DOI: https://doi.org/10.2210/pdb4IBO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-12-09 Released: 2012-12-26 
• Deposition Author(s): Vetting, M.W., Bouvier, J.T., Groninger-Poe, F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.187 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative gluconate dehydrogenase from agrobacterium tumefaciens (target EFI-506446)

Vetting, M.W., Bouvier, J.T., Groninger-Poe, F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (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: 117.16 kDa 
• Atom Count: 8,443 
• Modeled Residue Count: 1,016 
• Deposited Residue Count: 1,084 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gluconate dehydrogenase	A, B, C, D	271	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: Atu1407
UniProt
Find proteins for A9CJ43 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CJ43  Go to UniProtKB:  A9CJ43

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	F [auth A], G [auth B], I [auth C], K [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A], H [auth C], J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.187 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.783	α = 90
b = 135.783	β = 90
c = 126.165	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-26 
Deposition Author(s): Vetting, M.W., Bouvier, J.T., Groninger-Poe, F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description