9ZDO | pdb_00009zdo

Crystal structure of Zn-substituted rubredoxin from psychrophilic clostridia Clostridium psychrophilum

• PDB DOI: https://doi.org/10.2210/pdb9ZDO/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Clostridium psychrophilum
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-11-26 Released: 2026-05-06 
• Deposition Author(s): Doukov, T.I., George, D., Cole, C., Drumrigh, K., Jenney, F.E., Cramer, S.P.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.84 Å
• R-Value Free: 
  0.158 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Literature

Crystallography of Extremophile Proteins-Structural Comparisons of Psychrophilic and Hyperthermophilic Rubredoxins

Doukov, T., Turpin, T.F., George, D., Cole, C., Drumright, K., Rumley, M., Boyce, R., Jenney, F.E., Cramer, S.P.

(2026) Biomolecules 16: 623

• DOI: https://doi.org/10.3390/biom16050623

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.11 kDa 
• Atom Count: 537 
• Modeled Residue Count: 52 
• Deposited Residue Count: 52 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubredoxin	A	52	Clostridium psychrophilum	Mutation(s): 0

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], D [auth A], E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.84 Å
• R-Value Free:  0.158 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.477	α = 90
b = 37.02	β = 90
c = 40.715	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: 2026-05-06 
Deposition Author(s): Doukov, T.I., George, D., Cole, C., Drumrigh, K., Jenney, F.E., Cramer, S.P.

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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	GM65440
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM133894

Revision History  

• Version 1.0: 2026-05-06
  Type: Initial release