8EFZ

Crystal structure of CcNikZ-II, apoprotein

• PDB DOI: https://doi.org/10.2210/pdb8EFZ/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Clostridium carboxidivorans P7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-10 Released: 2024-03-13 
• Deposition Author(s): Stogios, P.J., Evdokimova, E., Diep, P., Yakunin, A., Mahadevan, K., Savchenko, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.259 
• R-Value Work: 0.222 
• R-Value Observed: 0.228 

Literature

Crystal structure of CcNikZ-II, apoprotein

Diep, P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 113.44 kDa 
• Atom Count: 7,955 
• Modelled Residue Count: 962 
• Deposited Residue Count: 994 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular solute-binding protein family 5	A, B	497	Clostridium carboxidivorans P7	Mutation(s): 0  Gene Names: CcarbDRAFT_1393
UniProt
Find proteins for C6PRH6 (Clostridium carboxidivorans P7) Explore C6PRH6  Go to UniProtKB:  C6PRH6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.259 
• R-Value Work: 0.222 
• R-Value Observed: 0.228 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.606	α = 90
b = 110.942	β = 113.72
c = 73.686	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MrBUMP	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-13 
Deposition Author(s): Stogios, P.J., Evdokimova, E., Diep, P., Yakunin, A., Mahadevan, K., Savchenko, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-13
  Type: Initial release