5AUR

Hydrogenobacter thermophilus cytochrome c552 dimer formed by domain swapping at N-terminal region

• PDB DOI: https://doi.org/10.2210/pdb5AUR/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Hydrogenobacter thermophilus TK-6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-08 Released: 2015-10-21 
• Deposition Author(s): Ren, C., Nagao, S., Yamanaka, M., Kamikubo, H., Komori, H., Shomura, Y., Higuchi, Y., Hirota, S.
• Funding Organization(s): JSPS

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Oligomerization enhancement and two domain swapping mode detection for thermostable cytochrome c552via the elongation of the major hinge loop.

Ren, C., Nagao, S., Yamanaka, M., Komori, H., Shomura, Y., Higuchi, Y., Hirota, S.

(2015) Mol Biosyst 11: 3218-3221

• PubMed: 26451671 
• DOI: https://doi.org/10.1039/c5mb00545k
• Primary Citation of Related Structures:  
  5AUR, 5AUS


• PubMed Abstract: 
  

  High-order oligomers of Hydrogenobacter thermophilus cytochrome c552 increased with the insertion of more Gly residues between Ala18 and Lys19 at the major hinge loop of the wild-type protein. N-Terminal domain swapping and C-terminal domain swapping were elucidated by using X-ray crystallography for the mutant with the insertion of three Gly residues at the hinge loop.

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Organizational Affiliation: 

Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.9 kDa 
• Atom Count: 2,938 
• Modelled Residue Count: 332 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-552	A, B [auth C], C [auth E], D [auth G]	83	Hydrogenobacter thermophilus TK-6	Mutation(s): 0  Gene Names: HTH_0988, Hydth_0984
UniProt
Find proteins for P15452 (Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6)) Explore P15452  Go to UniProtKB:  P15452

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	E [auth A], M [auth C], Q [auth E], S [auth G]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
IOD	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], N [auth C], O [auth C], P [auth C], R [auth E]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.85	α = 86.73
b = 42.898	β = 86.51
c = 53.591	γ = 89.83

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Ren, C., Nagao, S., Yamanaka, M., Kamikubo, H., Komori, H., Shomura, Y., Higuchi, Y., Hirota, S.

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Funding Organization	Location	Grant Number
JSPS	Japan	26288080
JSPS	Japan	15K13744

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2015-11-25
  Changes: Database references
• Version 1.2: 2020-02-19
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary