5JGW | pdb_00005jgw

Crystal structure of maize AKR4C13 in complex with NADP and acetate

• PDB DOI: https://doi.org/10.2210/pdb5JGW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Zea mays
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-20 Released: 2017-05-03 
• Deposition Author(s): Santos, M.L., Giuseppe, P.O., Kiyota, E., Sousa, S.M., Schmelz, E.A., Yunes, J.A., Koch, K.E., Murakami, M.T., Aparicio, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Crystal structure of maize AKR4C13 in complex with NADP and acetate

Sousa, S.M., Giuseppe, P.O., Murakami, M.T., Kiyota, E., Santos, M.L., Aparicio, R., Schmelz, E.A., Yunes, J.A., Koch, K.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

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

Biological Assembly 4  

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

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

Macromolecule Content 

• Total Structure Weight: 150.16 kDa 
• Atom Count: 10,096 
• Modeled Residue Count: 1,236 
• Deposited Residue Count: 1,308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldose reductase, AKR4C13	A, B, C, D	327	Zea mays	Mutation(s): 0  Gene Names: AR3
UniProt
Find proteins for E9JVD4 (Zea mays) Explore E9JVD4  Go to UniProtKB:  E9JVD4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], G [auth B], H [auth C], J [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
ACT	F [auth A], I [auth C], K [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.654	α = 90
b = 115.467	β = 90
c = 124.938	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Santos, M.L., Giuseppe, P.O., Kiyota, E., Sousa, S.M., Schmelz, E.A., Yunes, J.A., Koch, K.E., Murakami, M.T., Aparicio, R.

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Refinement description