5UHW | pdb_00005uhw

Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+ and Magnesium

• PDB DOI: https://doi.org/10.2210/pdb5UHW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhizobium rhizogenes K84
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-12 Released: 2017-01-25 
• Deposition Author(s): Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., Gerlt, J.A., Almo, S.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

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

Starting Model: experimental

Literature

Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+ and Magnesium

Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 76.35 kDa 
• Atom Count: 5,347 
• Modeled Residue Count: 684 
• Deposited Residue Count: 690 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase protein	A, B	345	Rhizobium rhizogenes K84	Mutation(s): 0  Gene Names: Arad_9238 EC: 1.1.1.420
UniProt
Find proteins for B9JK80 (Rhizobium rhizogenes (strain K84 / ATCC BAA-868)) Explore B9JK80  Go to UniProtKB:  B9JK80

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.216 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.674	α = 90
b = 112.856	β = 95.02
c = 65.741	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., Gerlt, J.A., Almo, S.C.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118303

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Structure summary
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description