9BKL | pdb_00009bkl

Cobalt substituted rubredoxin from Pyrococcus furiosus solved by Co/S-SAD

• PDB DOI: https://doi.org/10.2210/pdb9BKL/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-29 Released: 2024-06-05 
• Deposition Author(s): Zhou, D., Chen, L., Rose, J.P., Wang, B.C.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Literature

Cobalt substituted rubredoxin from Pyrococcus furiosus solved by Co/S-SAD

Zhou, D., Chen, L., Rose, J.P., Wang, B.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.09 kDa 
• Atom Count: 531 
• Modeled Residue Count: 54 
• Deposited Residue Count: 54 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubredoxin	A	54	Pyrococcus furiosus	Mutation(s): 0  Gene Names: rub, PF1282
UniProt
Find proteins for P24297 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore P24297  Go to UniProtKB:  P24297

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO (Subject of Investigation/LOI)	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.016	α = 90
b = 34.645	β = 90
c = 43.347	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Zhou, D., Chen, L., Rose, J.P., Wang, B.C.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release