7CGR | pdb_00007cgr

Crystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase E147A mutant (NADP and glycerol bound form)

• PDB DOI: https://doi.org/10.2210/pdb7CGR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Azospirillum brasilense
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-07-02 Released: 2020-07-29 
• Deposition Author(s): Yoshiwara, K., Watanabe, Y., Watanabe, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of bacterial L-arabinose 1-dehydrogenase in complex with L-arabinose and NADP+

Yoshiwara, K., Watanabe, S., Watanabe, Y.

(2020) Biochem Biophys Res Commun 530: 203-208

• DOI: https://doi.org/10.1016/j.bbrc.2020.07.071

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: 143.12 kDa 
• Atom Count: 10,288 
• Modeled Residue Count: 1,216 
• Deposited Residue Count: 1,276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-arabinose 1-dehydrogenase (NAD(P)(+))	A, B, C, D	319	Azospirillum brasilense	Mutation(s): 1  Gene Names: araA EC: 1.1.1.376 (PDB Primary Data), 1.1.1.120 (PDB Primary Data), 1.1.1.48 (PDB Primary Data)
UniProt
Find proteins for Q53TZ2 (Azospirillum brasilense) Explore Q53TZ2  Go to UniProtKB:  Q53TZ2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	E [auth A], H [auth B], I [auth C], J [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GOL	F [auth A], G [auth A], K [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.857	α = 90
b = 90.52	β = 101.93
c = 134.693	γ = 90

Software Package:

Software Name	Purpose
XDS	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-29 
Deposition Author(s): Yoshiwara, K., Watanabe, Y., Watanabe, S.

Revision History  

• Version 1.0: 2020-07-29
  Type: Initial release
  
• Version 1.1: 2020-08-12
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description