2YJ3 | pdb_00002yj3

Conformational changes in the catalytic domain of the CPx-ATPase CopB- B upon nucleotide binding

• PDB DOI: https://doi.org/10.2210/pdb2YJ3/pdb

• Classification: HYDROLASE
• Organism(s): Saccharolobus solfataricus P2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-05-18 Released: 2012-05-30 
• Deposition Author(s): Voellmecke, C., Schlicker, C., Luebben, M., Hofmann, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.284 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Conformational Changes in the Catalytic Domain of the Cpx-ATPase Copb-B Upon Nucleotide Binding

Voellmecke, C., Schlicker, C., Luebben, M., Hofmann, E.

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)

Macromolecule Content 

• Total Structure Weight: 29.14 kDa 
• Atom Count: 1,722 
• Modeled Residue Count: 236 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COPPER-TRANSPORTING ATPASE	A	263	Saccharolobus solfataricus P2	Mutation(s): 1  EC: 3.6.3.10
UniProt
Find proteins for Q97UU7 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97UU7  Go to UniProtKB:  Q97UU7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.284 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.98	α = 90
b = 52.59	β = 90
c = 68.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Voellmecke, C., Schlicker, C., Luebben, M., Hofmann, E.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description