6T9W | pdb_00006t9w

Crystal structure of formate dehydrogenase FDH2 D222A/Q223R enzyme from Granulicella mallensis MP5ACTX8 in complex with NADP and azide.

• PDB DOI: https://doi.org/10.2210/pdb6T9W/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Granulicella mallensis MP5ACTX8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-10-29 Released: 2020-08-05 
• Deposition Author(s): Robescu, M.S., Rubini, R., Filippini, F., Bergantino, B., Cendron, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.191 (DCC) 

Starting Model: experimental

Literature

From the Amelioration of a NADP+-dependent Formate Dehydrogenase to the Discovery of a New Enzyme: Round Trip from Theory to Practice

Robescu, M.S., Rubini, R., Beneventi, E., Tavanti, M., Lonigro, C., Zito, F., Filippini, F., Cendron, L., Bergantino, E.

(2020) ChemCatChem 

• DOI: https://doi.org/10.1002/cctc.201902089

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

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: 172.65 kDa 
• Atom Count: 12,872 
• Modeled Residue Count: 1,523 
• Deposited Residue Count: 1,544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A [auth B], B [auth A], C, D	386	Granulicella mallensis MP5ACTX8	Mutation(s): 2  Gene Names: AciX8_0868 EC: 1.17.1.9
UniProt
Find proteins for G8NTI5 (Granulicella mallensis (strain ATCC BAA-1857 / DSM 23137 / MP5ACTX8)) Explore G8NTI5  Go to UniProtKB:  G8NTI5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	E [auth B], G [auth A], I [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
AZI (Subject of Investigation/LOI)	F [auth B], H [auth A], J [auth C]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.191 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.53	α = 90
b = 62.08	β = 91.25
c = 211.745	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Robescu, M.S., Rubini, R., Filippini, F., Bergantino, B., Cendron, L.

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description