9WY9 | pdb_00009wy9

Pyrococcus furiosus FdxA D14H variant

PDB DOI: https://doi.org/10.2210/pdb9WY9/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Pyrococcus furiosus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-09-26 Released: 2026-10-14
Deposition Author(s): Yoshida, R., Fujishiro, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.245 (Depositor), 0.243 (DCC)
R-Value Work:
0.191 (Depositor), 0.190 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Change in polarity of FeS of ferredoxin

Yoshida, R., Fujishiro, T.

To be published.

Macromolecule Content

Total Structure Weight: 7.49 kDa
Atom Count: 539
Modeled Residue Count: 66
Deposited Residue Count: 66
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin	A	66	Pyrococcus furiosus	Mutation(s): 1 Gene Names: fdxA, PF1909
UniProt
Find proteins for P29603 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore P29603 Go to UniProtKB: P29603
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29603
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F3S (Subject of Investigation/LOI) Query on F3S Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.245 (Depositor), 0.243 (DCC)
R-Value Work: 0.191 (Depositor), 0.190 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.88	α = 90
b = 77.88	β = 90
c = 40.66	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-10-14
Type: Initial release