7VOS

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
R-Value Work: 0.074
R-Value Observed: 0.074

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

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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abn2276
Primary Citation of 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
Modelled Residue Count: 83
Deposited Residue Count: 83
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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]	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 F [auth A] SDF format, chain G [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [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 K [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 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]	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 O [auth A] SDF format, chain P [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [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
R-Value Work: 0.074
R-Value Observed: 0.074
Space Group: P 2₁ 2₁ 2₁

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

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	--