8JVP

Crystal structure of the dimeric DZBB fold protein Ph1

• PDB DOI: https://doi.org/10.2210/pdb8JVP/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-06-28 Released: 2024-07-03 
• Deposition Author(s): Yagi, S., Tagami, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.225 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 

Starting Model: in silico

Literature

Missing-link fold reveals the evolutionary pathway between RNA polymerase and ribosomal proteins

Yagi, S., Tagami, S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 5.23 kDa 
• Atom Count: 428 
• Modelled Residue Count: 48 
• Deposited Residue Count: 48 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ph1	A	48	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.225 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.056	α = 90
b = 35.056	β = 90
c = 54.844	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Yagi, S., Tagami, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18H01328
Japan Society for the Promotion of Science (JSPS)	Japan	20K15854
Japan Society for the Promotion of Science (JSPS)	Japan	22H01346

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release