2Z1N

Crystal structure of APE0912 from Aeropyrum pernix K1

• PDB DOI: https://doi.org/10.2210/pdb2Z1N/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-10 Released: 2008-03-18 
• Deposition Author(s): Ichimura, T., Yamamura, A., Mimoto, F., Ohtsuka, J., Miyazono, K., Okai, M., Kamo, M., Lee, W.-C., Nagata, K., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

A unique catalytic triad revealed by the crystal structure of APE0912, a short-chain dehydrogenase/reductase family protein from Aeropyrum pernix K1

Yamamura, A., Ichimura, T., Mimoto, F., Ohtsuka, J., Miyazono, K., Okai, M., Kamo, M., Lee, W.-C., Nagata, K., Tanokura, M.

(2008) Proteins 70: 1640-1645

• PubMed: 18175326 
• DOI: https://doi.org/10.1002/prot.21860
• Primary Citation of Related Structures:  
  2Z1N

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Organizational Affiliation: 

Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.

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.

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.76 kDa 
• Atom Count: 3,897 
• Modelled Residue Count: 480 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dehydrogenase	A, B	260	Aeropyrum pernix K1	Mutation(s): 0
UniProt
Find proteins for Q9YDK1 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YDK1  Go to UniProtKB:  Q9YDK1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.759	α = 90
b = 68.869	β = 119
c = 69.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Ichimura, T., Yamamura, A., Mimoto, F., Ohtsuka, J., Miyazono, K., Okai, M., Kamo, M., Lee, W.-C., Nagata, K., Tanokura, M.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description