3WDS | pdb_00003wds

Crystal structure of 3-quinuclidinone reductase from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb3WDS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Agrobacterium tumefaciens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-22 Released: 2014-06-25 
• Deposition Author(s): Hou, F., Miyakawa, T., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Structural basis for high substrate-binding affinity of 3-quinuclidinone reductase AtQR

Hou, F., Miyakawa, T., Kataoka, M., Takeshita, D., Kumashiro, S., Nagata, K., Shimizu, S., Tanokura, M.

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: 112.65 kDa 
• Atom Count: 8,271 
• Modeled Residue Count: 1,028 
• Deposited Residue Count: 1,052 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-dependent quinuclidinone reductase	A, B, C [auth D], D [auth C]	263	Agrobacterium tumefaciens	Mutation(s): 0
UniProt
Find proteins for G1K3P5 (Agrobacterium tumefaciens) Explore G1K3P5  Go to UniProtKB:  G1K3P5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], H [auth B], K [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO	G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	F [auth A], I [auth B], J [auth D], L [auth C]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.97	α = 90
b = 126.37	β = 110.5
c = 62.02	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Hou, F., Miyakawa, T., Tanokura, M.

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description