4NMJ | pdb_00004nmj

Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+ at 2 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4NMJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrobaculum ferrireducens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-15 Released: 2014-11-19 
• Deposition Author(s): Petrova, T., Boyko, K.M., Bezsudnova, E.Y., Mardanov, A.V., Gumerov, V.M., Ravin, N.V., Popov, V.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+ at 2 A resolution

Petrova, T., Boyko, K.M., Bezsudnova, E.Y., Mardanov, A.V., Gumerov, V.M., Ravin, N.V., 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)

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)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 441.62 kDa 
• Atom Count: 33,717 
• Modeled Residue Count: 3,880 
• Deposited Residue Count: 3,928 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase	A, B, C, D, E, F, G, H	491	Pyrobaculum ferrireducens	Mutation(s): 0  Gene Names: P186_1147 EC: 1.2.1
UniProt
Find proteins for G7VCG0 (Pyrobaculum ferrireducens) Explore G7VCG0  Go to UniProtKB:  G7VCG0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.479	α = 90
b = 184.394	β = 90
c = 207.753	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Petrova, T., Boyko, K.M., Bezsudnova, E.Y., Mardanov, A.V., Gumerov, V.M., Ravin, N.V., Popov, V.O.

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description