7YL8 | pdb_00007yl8

Neutron structure of Bacillus thermoproteolyticus Ferredoxin at room temperature

PDB DOI: https://doi.org/10.2210/pdb7YL8/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Bacillus thermoproteolyticus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-07-25 Released: 2024-02-07
Deposition Author(s): Unno, M., Wada, K., Kobayashi, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.157 (Depositor), 0.156 (DCC)
R-Value Work:
0.139 (Depositor), 0.139 (DCC)
R-Value Observed:
0.140 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.184 (Depositor)
R-Value Work:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7YL8

This is version 1.3 of the entry. See complete history.

Literature

Protonation/deprotonation-driven switch for the redox stability of the low-potential [4Fe-4S] ferredoxin

Wada, K., Kobayashi, K., Era, I., Isobe, Y., Kamimura, T., Marukawa, M., Nagae, T., Honjo, K., Kaseda, N., Motoyama, Y., Inoue, K., Sugishima, M., Kusaka, K., Yano, N., Fukuyama, K., Mishima, M., Kitagawa, Y., Unno, M.

(2025) Elife

DOI: https://doi.org/10.7554/eLife.102506.2

Macromolecule Content

Total Structure Weight: 9.13 kDa
Atom Count: 740
Modeled Residue Count: 81
Deposited Residue Count: 81
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin	A	81	Bacillus thermoproteolyticus	Mutation(s): 0
UniProt
Find proteins for P10245 (Bacillus thermoproteolyticus) Explore P10245 Go to UniProtKB: P10245
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10245
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 (Subject of Investigation/LOI) Query on SF4 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]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.157 (Depositor), 0.156 (DCC)
R-Value Work: 0.139 (Depositor), 0.139 (DCC)
R-Value Observed: 0.140 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.184 (Depositor)
R-Value Work: 0.162 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.43	α = 90
b = 37.91	β = 105.96
c = 33.01	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	24570122
Japan Society for the Promotion of Science (JSPS)	Japan	20H03196

Revision History (Full details and data files)

Version 1.0: 2024-02-07
Type: Initial release
Version 1.1: 2025-02-19
Changes: Database references, Structure summary
Version 1.2: 2026-03-04
Changes: Refinement description
Version 1.3: 2026-08-12
Type: Remediation
Reason: Metalloprotein remediation
Changes: Derived calculations, Structure summary