5AUR

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1039/c5mb00545k
  • Primary Citation of Related Structures:  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 ...

    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.


    Organizational Affiliation

    Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan. hirota@ms.naist.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-552
A, C, E, G
83Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6)N/A
Find proteins for P15452 (Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6))
Go to UniProtKB:  P15452
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, C, E
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
A, C, E, G
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 32.850α = 86.73
b = 42.898β = 86.51
c = 53.591γ = 89.83
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
JSPSJapan26288080
JSPSJapan15K13744

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-25
    Type: Database references