5AUS

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

PDB DOI: https://doi.org/10.2210/pdb5AUS/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., Komori, H., Shomura, Y., Higuchi, Y., Hirota, S.
Funding Organization(s): JSPS

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.202
R-Value Work: 0.171
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 26451671 Search on PubMed
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.

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.

Macromolecule Content

Total Structure Weight: 18.75 kDa
Atom Count: 1,553
Modelled Residue Count: 162
Deposited Residue Count: 166
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-552	A, B [auth C]	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15452
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth C] MOL2 format, chain C [auth A] MOL2 format, chain D [auth C]	C [auth A], D [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth C] Interactions & Density Focus chain C [auth A] Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.202
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71	α = 90
b = 71.02	β = 90
c = 62.08	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-10-21

Deposition Author(s):

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

Revision History (Full details and data files)

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