2YJ6 | pdb_00002yj6

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

• PDB DOI: https://doi.org/10.2210/pdb2YJ6/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: 
  0.287 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.242 (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)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.06 kDa 
• Atom Count: 3,853 
• Modeled Residue Count: 500 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COPPER-TRANSPORTING ATPASE	A, B	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A99	C [auth A], D [auth B]	5'-O-[(S)-hydroxy{[(R)-hydroxy({(S)-hydroxy[(1S)-1-(2-nitrophenyl)ethoxy]phosphoryl}oxy)phosphoryl]oxy}phosphoryl]adenosine C18 H23 N6 O15 P3 UOLVQBSMMHANLG-YBGGAFRISA-N
PO4	E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.287 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.56	α = 90
b = 53.9	β = 98.24
c = 78.95	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