7VOS | pdb_00007vos

High-resolution neutron and X-ray joint refined structure of high-potential iron-sulfur protein in the oxidized state

PDB DOI: https://doi.org/10.2210/pdb7VOS/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Thermochromatium tepidum
Mutation(s): No

Deposited: 2021-10-14 Released: 2022-06-01
Deposition Author(s): Hanazono, Y., Hirano, Y., Takeda, K., Kusaka, K., Tamada, T., Miki, K.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.66 Å
R-Value Free:
0.082 (Depositor)
R-Value Work:
0.074 (Depositor)
R-Value Observed:
0.074 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.168 (Depositor)
R-Value Work:
0.154 (Depositor)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis.

Hanazono, Y., Hirano, Y., Takeda, K., Kusaka, K., Tamada, T., Miki, K.

(2022) Sci Adv 8: eabn2276-eabn2276

PubMed: 35594350 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abn2276
Primary Citation Related Structures:
7VOS

PubMed Abstract:
The planarity of the peptide bond is important for the stability and structure formation of proteins. However, substantial distortion of peptide bonds has been reported in several high-resolution structures and computational analyses. To investigate the peptide bond planarity, including hydrogen atoms, we report a 1.2-Å resolution neutron structure of the oxidized form of high-potential iron-sulfur protein. This high-resolution neutron structure shows that the nucleus positions of the amide protons deviate from the peptide plane and shift toward the acceptors. The planarity of the H─N─C═O plane depends strongly on the pyramidalization of the nitrogen atom. Moreover, the orientation of the amide proton of Cys ⁷⁵ is different in the reduced and oxidized states, possibly because of the electron storage capacity of the iron-sulfur cluster.

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.

Macromolecule Content

Total Structure Weight: 10.18 kDa
Atom Count: 959
Modeled Residue Count: 83
Deposited Residue Count: 83
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High-potential iron-sulfur protein	A	83	Thermochromatium tepidum	Mutation(s): 0
UniProt
Find proteins for P80176 (Thermochromatium tepidum) Explore P80176 Go to UniProtKB: P80176
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80176
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
D3O Query on D3O Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	trideuteriooxidanium D₃ O XLYOFNOQVPJJNP-ZRLBSURWSA-O		Interactions Focus chain Q [auth A]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	M [auth A], N [auth A], O [auth A], P [auth A]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.66 Å
R-Value Free: 0.082 (Depositor)
R-Value Work: 0.074 (Depositor)
R-Value Observed: 0.074 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.168 (Depositor)
R-Value Work: 0.154 (Depositor)
R-Value Observed: 0.154 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.334	α = 90
b = 58.855	β = 90
c = 23.548	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
MOLREP	phasing
HKL-2000	data collection

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	--
Japan Science and Technology	Japan	--
Japan Society for the Promotion of Science (JSPS)	Japan	--