9Y2E | pdb_00009y2e

Rubredoxin from Pyrococcus Furiosus at 100K, formyl-Methionine N-terminus

• PDB DOI: https://doi.org/10.2210/pdb9Y2E/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia phage E20
• Mutation(s): No 


• Deposited: 2025-09-01 Released: 2026-04-29 
• Deposition Author(s): Doukov, T., Cramer, S.P.J., George, D., Jenney, F.E.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.78 Å
• R-Value Free: 
  0.140 (Depositor), 0.145 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Literature

Some Like It Hot -Structural Changes in Extremophile Rubredoxin at 120 °C.

Doukov, T., Leontyev, I., Jenney Jr., F.E., George, D., Cramer, S.P.

(2026) Angew Chem Int Ed Engl 65: e20302-e20302

• PubMed: 41287388 
• DOI: https://doi.org/10.1002/anie.202520302
• Primary Citation Related Structures: 
  9XZU, 9Y00, 9Y0Y, 9Y0Z, 9Y11, 9Y1U, 9Y28, 9Y29, 9Y2E, 9Y2G, 9Y2Y, 9Y30, 9Y32, 9Y33, 9Y37, 9Y38


• PubMed Abstract: 
  

  How does the structure of a protein change as the temperature is raised from cryogenic conditions at 100 K to 393 K? Understanding the structure and dynamics of proteins under environmental extremes is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Here we reveal the high temperature crystal structure of a hyperthermophilic (Pyrococcus furiosus) rubredoxin at 393 K (120 °C), together with multiple complementary structures down to 100 K. The results are compared with molecular dynamics calculations. Significant changes in H-bonding are observed. Discussions about high-temperature protein structure and stability need to recognize that low temperature structures may not represent the high temperature case.

---

Organizational Affiliation: 
• SSRL, SLAC National Laboratory, Menlo Park, CA, 94025, USA.
SETI Institute, Mountain View, CA, 94043, USA.
Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA, 30024, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 6.16 kDa 
• Atom Count: 596 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K (Subject of Investigation/LOI)	C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	A	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.78 Å
• R-Value Free:  0.140 (Depositor), 0.145 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.961	α = 90
b = 34.403	β = 90
c = 43.365	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
Aimless	data scaling
HKL2Map	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-29 
Deposition Author(s): Doukov, T., Cramer, S.P.J., George, D., Jenney, F.E.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-2149122
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-65440

Revision History  

• Version 1.0: 2026-04-29
  Type: Initial release