9ZDP | pdb_00009zdp

Crystal structure of rubredoxin from psychrophilic bacterium Polaromonas glacialis

PDB DOI: https://doi.org/10.2210/pdb9ZDP/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Polaromonas glacialis
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., Drumright, 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.201 (Depositor), 0.209 (DCC)
R-Value Work:
0.171 (Depositor), 0.182 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 42.5 kDa
Atom Count: 3,146
Modeled Residue Count: 371
Deposited Residue Count: 371
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubredoxin	A, B, C, D, E A, B, C, D, E, F, G	53	Polaromonas glacialis	Mutation(s): 0 Gene Names: ABLV49_04330
UniProt
Find proteins for A0AAU7LTP7 (Polaromonas hydrogenivorans) Explore A0AAU7LTP7 Go to UniProtKB: A0AAU7LTP7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAU7LTP7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain O [auth G] SDF format, chain N [auth F] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain O [auth G] MOL2 format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain O [auth G] mmCIF format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	H [auth A] I [auth B] K [auth C] L [auth D] M [auth E] H [auth A], I [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.201 (Depositor), 0.209 (DCC)
R-Value Work: 0.171 (Depositor), 0.182 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.897	α = 90
b = 73.897	β = 90
c = 199.351	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-06

Deposition Author(s):

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