8YTR

The structure of Cu(II)-CopC from Thioalkalivibrio paradoxus

• PDB DOI: https://doi.org/10.2210/pdb8YTR/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Thioalkalivibrio paradoxus ARh 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-26 Released: 2024-04-24 
• Deposition Author(s): Kulikova, O.G., Solovieva, A.Y., Varfolomeeva, L.A., Dergousova, N.I., Nikolaeva, A.Y., Boyko, K.M., Tikhonova, T.V., Popov, V.O.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

The structure of Cu(II)-CopC from Thioalkalivibrio paradoxus

Kulikova, O.G., Solovieva, A.Y., Varfolomeeva, L.A., Dergousova, N.I., Nikolaeva, A.Y., Boyko, K.M., Tikhonova, T.V., Popov, V.O.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 28.52 kDa 
• Atom Count: 2,061 
• Modelled Residue Count: 253 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CopC domain-containing protein	A, B	130	Thioalkalivibrio paradoxus ARh 1	Mutation(s): 0  Gene Names: THITH_13340
UniProt
Find proteins for W0DSL1 (Thioalkalivibrio paradoxus ARh 1) Explore W0DSL1  Go to UniProtKB:  W0DSL1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A], D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	F [auth A], G [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.241	α = 90
b = 38.275	β = 90.33
c = 104.666	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-24 
Deposition Author(s): Kulikova, O.G., Solovieva, A.Y., Varfolomeeva, L.A., Dergousova, N.I., Nikolaeva, A.Y., Boyko, K.M., Tikhonova, T.V., Popov, V.O.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-24
  Type: Initial release