9JVE | pdb_00009jve

Crysral structure of 2-keto-3-deoxypentonate 4-dehydrogenase from Herbaspirillum huttiense (apo form)

• PDB DOI: https://doi.org/10.2210/pdb9JVE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Herbaspirillum huttiense
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2024-10-09 Released: 2025-10-15 
• Deposition Author(s): Watanabe, S., Akagashi, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.234 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: in silico

Literature

2-keto-3-deoxypentonate 4-dehydrogenase

Watanabe, S., Akagashi, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.7 kDa 
• Atom Count: 3,802 
• Modeled Residue Count: 490 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SDR family NAD(P)-dependent oxidoreductase	A, B	261	Herbaspirillum huttiense	Mutation(s): 0  Gene Names: RI046_07315
UniProt
Find proteins for A0AAJ2H7U7 (Herbaspirillum huttiense) Explore A0AAJ2H7U7  Go to UniProtKB:  A0AAJ2H7U7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.234 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.942	α = 90
b = 84.948	β = 103.36
c = 69.722	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Watanabe, S., Akagashi, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release