7QZL | pdb_00007qzl

Amine Dehydrogenase from Cystobacter fuscus (CfusAmDH) W145A mutant with NADP+ and pentylamine

• PDB DOI: https://doi.org/10.2210/pdb7QZL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cystobacter fuscus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-01-31 Released: 2022-12-07 
• Deposition Author(s): Bennett, M., Ducrot, L., Vaxelaire-Vergne, C., Grogan, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Cover Feature: Expanding the Substrate Scope of Native Amine Dehydrogenases through In Silico Structural Exploration and Targeted Protein Engineering (ChemCatChem 22/2022)

Ducrot, L., Bennett, M., Andre-Leroux, G., Elisee, E., Marynberg, S., Fossey-Jouenne, A., Zaparucha, A., Grogan, G., Vergne-Vaxelaire, C.

(2022) ChemCatChem 14

• DOI: https://doi.org/10.1002/cctc.202201257

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 76.49 kDa 
• Atom Count: 5,845 
• Modeled Residue Count: 682 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amine Dehydrogenase	A [auth D], B [auth A]	346	Cystobacter fuscus	Mutation(s): 1  Gene Names: D187_009359
UniProt
Find proteins for S9Q235 (Cystobacter fuscus (strain ATCC 25194 / DSM 2262 / NBRC 100088 / M29)) Explore S9Q235  Go to UniProtKB:  S9Q235

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth D], F [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
TRS	D, G [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
AML (Subject of Investigation/LOI)	E [auth D], H [auth A]	AMYLAMINE C5 H13 N DPBLXKKOBLCELK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.691	α = 90
b = 84.31	β = 90
c = 284.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-07 
Deposition Author(s): Bennett, M., Ducrot, L., Vaxelaire-Vergne, C., Grogan, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-12-07
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description