7VOS

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


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 1.0 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

  • DOI: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
High-potential iron-sulfur proteinA83Thermochromatium tepidumMutation(s): 0 
Gene Names: hip
UniProt
Find proteins for P80176 (Thermochromatium tepidum)
Explore P80176 
Go to UniProtKB:  P80176
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80176
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
B [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
D3O
Query on D3O

Download Ideal Coordinates CCD File 
Q [auth A]trideuteriooxidanium
D3 O
XLYOFNOQVPJJNP-ZRLBSURWSA-O
 Ligand Interaction
NH4
Query on NH4

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A],
O [auth A],
P [auth A]
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
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 = 46.334α = 90
b = 58.855β = 90
c = 23.548γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOLREPphasing
HKL-2000data collection

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release