7F7M | pdb_00007f7m

AKR4C17 in complex with NADP+ and glyphosate

• PDB DOI: https://doi.org/10.2210/pdb7F7M/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Echinochloa colona
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-06-30 Released: 2022-07-06 
• Deposition Author(s): Li, H., Yang, Y., Hu, Y., Chen, C.-C., Huang, J.-W., Min, J., Dai, L., Guo, R.-T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structural analysis and engineering of aldo-keto reductase from glyphosate-resistant Echinochloa colona

Li, H., Yang, Y., Hu, Y., Chen, C.C., Huang, J.W., Min, J., Dai, L., Guo, R.T.

(2022) J Hazard Mater 436: 129191

• DOI: https://doi.org/10.1016/j.jhazmat.2022.129191

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 72.54 kDa 
• Atom Count: 5,167 
• Modeled Residue Count: 618 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AKR4-2	A, B	321	Echinochloa colona	Mutation(s): 0
UniProt
Find proteins for A0A5J6VLZ7 (Echinochloa colona) Explore A0A5J6VLZ7  Go to UniProtKB:  A0A5J6VLZ7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	D [auth A], G [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GPJ (Subject of Investigation/LOI)	C [auth A]	GLYPHOSATE C3 H9 N O5 P XDDAORKBJWWYJS-UHFFFAOYSA-O
SO4	E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.64	α = 90
b = 77.64	β = 90
c = 451.888	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Li, H., Yang, Y., Hu, Y., Chen, C.-C., Huang, J.-W., Min, J., Dai, L., Guo, R.-T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2021YFC2100300

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description