7DON

Structure of tubulin H392D mutant from Odinarchaeota

• PDB DOI: https://doi.org/10.2210/pdb7DON/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Candidatus Odinarchaeum yellowstonii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-12-14 Released: 2021-12-22 
• Deposition Author(s): Robinson, R.C., Akil, C.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.208 
• R-Value Work: 0.171 

Starting Model: experimental

Literature

Structure of tubulin H392D mutant from Odinarchaeota

Robinson, R.C., Akil, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 48.65 kDa 
• Atom Count: 3,649 
• Modelled Residue Count: 423 
• Deposited Residue Count: 425 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin-like protein CetZ	A [auth B]	425	Candidatus Odinarchaeum yellowstonii	Mutation(s): 1  Gene Names: cetZ, OdinLCB4_01330

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	B	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	C [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	D [auth B], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.208 
• R-Value Work: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.21	α = 90
b = 92.614	β = 90
c = 102.143	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Robinson, R.C., Akil, C.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR19S5

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description