8Y83

Crystal structure of a ketoreductase from Sphingobacterium siyangense SY1 with co-enzyme

• PDB DOI: https://doi.org/10.2210/pdb8Y83/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sphingobacterium siyangense
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-02-05 Released: 2024-06-12 
• Deposition Author(s): Zheng, Z.R., Wei, H.L., Liu, W.D., You, S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.201 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Starting Model: in silico

Literature

Crystal structure of a ketoreductase from Sphingobacterium siyangense SY1 with co-enzyme

Zheng, Z.R., Wei, H.L., Liu, W.D., You, S.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 53.22 kDa 
• Atom Count: 3,836 
• Modelled Residue Count: 494 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family)	A, B	249	Sphingobacterium siyangense	Mutation(s): 0  Gene Names: IQ31_01205
UniProt
Find proteins for A0A562MSV3 (Sphingobacterium siyangense) Explore A0A562MSV3  Go to UniProtKB:  A0A562MSV3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.201 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.434	α = 90
b = 84.434	β = 90
c = 280.321	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Zheng, Z.R., Wei, H.L., Liu, W.D., You, S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release