8X1K | pdb_00008x1k

Structure of RvY_06210 at 2.55 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb8X1K/pdb

• Classification: HYDROLASE
• Organism(s): Ramazzottius varieornatus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-08 Released: 2024-11-13 
• Deposition Author(s): Kato, S., Fukuda, Y., Inoue, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.270 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Metabolite phosphatase from anhydrobiotic tardigrades

Kato, S., Fukuda, Y., Inoue, T.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 66.91 kDa 
• Atom Count: 4,097 
• Modeled Residue Count: 554 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RvY_06210	A, B	313	Ramazzottius varieornatus	Mutation(s): 0  Gene Names: RvY_06210-1
UniProt
Find proteins for A0A1D1V463 (Ramazzottius varieornatus) Explore A0A1D1V463  Go to UniProtKB:  A0A1D1V463

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.270 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.152	α = 90
b = 80.372	β = 90
c = 105.025	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-13 
Deposition Author(s): Kato, S., Fukuda, Y., Inoue, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2024-11-13
  Type: Initial release
  
• Version 1.1: 2025-12-03
  Changes: Database references