3NAQ | pdb_00003naq

Apo-form of NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb3NAQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-02 Released: 2010-07-07 
• Deposition Author(s): Shabalin, I.G., Polyakov, K.M., Serov, A.E., Skirgello, O.E., Sadykhov, E.G., Dorovatovskiy, P.V., Tishkov, V.I., Popov, V.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.197 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Structures of the apo and holo forms of NAD-dependent formate dehydrogenase from the higher-plant Arabidopsis Thaliana

Shabalin, I.G., Polyakov, K.M., Skirgello, O.E., Tishkov, V.I., Popov, V.O.

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)

Macromolecule Content 

• Total Structure Weight: 79.68 kDa 
• Atom Count: 6,031 
• Modeled Residue Count: 702 
• Deposited Residue Count: 714 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A, B	357	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At5g14780, FDH, FDH1, T9L3_80 EC: 1.2.1.2 (PDB Primary Data), 1.17.1.9 (UniProt)
UniProt
Find proteins for Q9S7E4 (Arabidopsis thaliana) Explore Q9S7E4  Go to UniProtKB:  Q9S7E4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.197 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.33	α = 90
b = 106.23	β = 90
c = 106.5	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-07 
Deposition Author(s): Shabalin, I.G., Polyakov, K.M., Serov, A.E., Skirgello, O.E., Sadykhov, E.G., Dorovatovskiy, P.V., Tishkov, V.I., Popov, V.O.

Revision History  

• Version 1.0: 2010-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations