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
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Procambarus clarkii Arginine kinase

Yang, Y., Jin, T.C.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H6VGI2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-09

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.