8IYU

CfbA S11T variant with Ni(II) ions

• PDB DOI: https://doi.org/10.2210/pdb8IYU/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-04-06 Released: 2024-04-10 
• Deposition Author(s): Ogawa, S., Fujishiro, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.204 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

Substrate selectivity of CfbA

Ogawa, S., Hikita, M., Fujishiro, 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 33.25 kDa 
• Atom Count: 1,952 
• Modelled Residue Count: 239 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sirohydrochlorin cobaltochelatase	A, B	143	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 1  Gene Names: cbiX, cfbA, MJ0970 EC: 4.99.1.11 (UniProt), 4.99.1.3 (UniProt)
UniProt
Find proteins for Q58380 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58380  Go to UniProtKB:  Q58380

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A], D [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.204 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.18	α = 90
b = 67.18	β = 90
c = 84.11	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Ogawa, S., Fujishiro, T.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19H04639

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release