7DJS | pdb_00007djs

Crystal structure of isopiperitenol dehydrogenase from Pseudomonas aeruginosa complexed with NAD

• PDB DOI: https://doi.org/10.2210/pdb7DJS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-11-21 Released: 2021-09-15 
• Deposition Author(s): Zhan, J.R., Zheng, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.186 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Discovery and Engineering of Bacterial (-)-Isopiperitenol Dehydrogenases to Enhance (-)-Menthol Precursor Biosynthesis.

Zhan, J.R., Shou, C., Zheng, Y.C., Chen, Q., Pan, J., Li, C.X., Xu, J.H.

(2021) Adv Synth Catal 363: 3973-3982

• DOI: https://doi.org/10.1002/adsc.202100368

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: 109.9 kDa 
• Atom Count: 7,896 
• Modeled Residue Count: 964 
• Deposited Residue Count: 1,044 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SDR family oxidoreductase	A, B, C, D	261	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: DY930_09865, F7O90_18305, FDK04_18370, IPC116_19850, IPC36_02985
UniProt
Find proteins for A0A554HE32 (Pseudomonas aeruginosa) Explore A0A554HE32  Go to UniProtKB:  A0A554HE32

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.186 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.201	α = 90
b = 108.582	β = 90
c = 124.609	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-15 
Deposition Author(s): Zhan, J.R., Zheng, Y.C.

Revision History  

• Version 1.0: 2021-09-15
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description