7ARZ

Ternary complex of NAD-dependent formate dehydrogenase from Physcomitrium patens

• PDB DOI: https://doi.org/10.2210/pdb7ARZ/pdb

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


• Deposited: 2020-10-26 Released: 2021-11-03 
• Deposition Author(s): Goryaynova, D.A., Nikolaeva, A.Y., Pometun, A.A., Savin, S.S., Parshin, P.D., Popov, V.O., Tishkov, V.I., Boyko, K.M.
• Funding Organization(s): Russian Foundation for Basic Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Ternary complex of NAD-dependent formate dehydrogenase from Physcomitrium patens

Boyko, K.M., Pometun, A.A., Goryaynova, D.A., Nikolaeva, A.Y., Parshin, P.D., Popov, V.O., Tishkov, V.I.

To be published.

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: 40.47 kDa 
• Atom Count: 2,975 
• Modelled Residue Count: 361 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase, mitochondrial	A	361	Physcomitrium patens	Mutation(s): 0  Gene Names: PHYPA_020821, PHYPADRAFT_214795 EC: 1.17.1.9
UniProt
Find proteins for A9SQZ2 (Physcomitrium patens) Explore A9SQZ2  Go to UniProtKB:  A9SQZ2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
AZI (Subject of Investigation/LOI)	C [auth A], D [auth A]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.36	α = 90
b = 68.36	β = 90
c = 203.44	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-03 
Deposition Author(s): Goryaynova, D.A., Nikolaeva, A.Y., Pometun, A.A., Savin, S.S., Parshin, P.D., Popov, V.O., Tishkov, V.I., Boyko, K.M.

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Funding Organization	Location	Grant Number
Russian Foundation for Basic Research	Russian Federation	18-34-20098

Revision History  

• Version 1.0: 2021-11-03
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description