8YX0 | pdb_00008yx0

Crystal structure of Procambarus clarkii Arginine kinase

• PDB DOI: https://doi.org/10.2210/pdb8YX0/pdb

• Classification: ALLERGEN
• Organism(s): Procambarus clarkii
• Mutation(s): No 


• Deposited: 2024-04-01 Released: 2025-04-09 
• Deposition Author(s): Yang, Y., Jin, T.C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.217 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Procambarus clarkii Arginine kinase

Yang, Y., Jin, T.C.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.04 kDa 
• Atom Count: 2,968 
• Modeled Residue Count: 349 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginine kinase Pro c 2.0101	A	356	Procambarus clarkii	Mutation(s): 0  EC: 2.7.3.3
UniProt
Find proteins for H6VGI2 (Procambarus clarkii) Explore H6VGI2  Go to UniProtKB:  H6VGI2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.217 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.74	α = 90
b = 59.9	β = 90
c = 140.12	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: 2025-04-09 
Deposition Author(s): Yang, Y., Jin, T.C.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31901811

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release