5UHZ | pdb_00005uhz

Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, D-Apionate and Magnesium

• PDB DOI: https://doi.org/10.2210/pdb5UHZ/pdb

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


• Deposited: 2017-01-12 Released: 2017-02-01 
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+, D-Apionate 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: 76.65 kDa 
• Atom Count: 5,376 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
89Y	D [auth A], G [auth B]	(3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-one C5 H8 O5 MTSAHRPUAGVYCZ-WVZVXSGGSA-N
MG	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.763	α = 90
b = 114.183	β = 94.99
c = 66.158	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., Gerlt, J.A., Almo, S.C.

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

Revision History  

• Version 1.0: 2017-02-01
  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 2.0: 2020-05-13
  Changes: Atomic model
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 2.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description