6AIR | pdb_00006air

High resolution structure of perdeuterated high-potential iron-sulfur protein

• PDB DOI: https://doi.org/10.2210/pdb6AIR/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Thermochromatium tepidum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-24 Released: 2019-08-21 
• Deposition Author(s): Hanazono, Y., Takeda, K., Miki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.85 Å
• R-Value Free: 
  0.107 (Depositor), 0.106 (DCC) 
• R-Value Work: 
  0.096 (Depositor), 0.095 (DCC) 

Starting Model: experimental

Literature

Characterization of perdeuterated high-potential iron-sulfur protein with high-resolution X-ray crystallography.

Hanazono, Y., Takeda, K., Miki, K.

(2020) Proteins 88: 251-259

• PubMed: 31365157 
• DOI: https://doi.org/10.1002/prot.25793
• Primary Citation Related Structures: 
  6AIQ, 6AIR


• PubMed Abstract: 
  

  Perdeuteration in neutron crystallography is an effective method for determining the positions of hydrogen atoms in proteins. However, there is shortage of evidence that the high-resolution details of perdeuterated proteins are consistent with those of the nondeuterated proteins. In this study, we determined the X-ray structure of perdeuterated high-potential iron-sulfur protein (HiPIP) at a high resolution of 0.85 å resolution. The comparison of the nondeuterated and perdeuterated structures of HiPIP revealed slight differences between the two structures. The spectroscopic and spectroelectrochemical studies also showed that perdeuterated HiPIP has approximately the same characteristics as nondeuterated HiPIP. These results further emphasize the suitability of using perdeuterated proteins in the high-resolution neutron crystallography.

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Organizational Affiliation: 
• Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 9.81 kDa 
• Atom Count: 840 
• Modeled Residue Count: 83 
• Deposited Residue Count: 83 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High-potential iron-sulfur protein	A	83	Thermochromatium tepidum	Mutation(s): 0  Gene Names: hip
UniProt
Find proteins for P80176 (Thermochromatium tepidum) Explore P80176  Go to UniProtKB:  P80176

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.85 Å
• R-Value Free:  0.107 (Depositor), 0.106 (DCC) 
• R-Value Work:  0.096 (Depositor), 0.095 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.287	α = 90
b = 58.723	β = 90
c = 23.489	γ = 90

Software Package:

Software Name	Purpose
SHELXL	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Hanazono, Y., Takeda, K., Miki, K.

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description