8GME

Crystal structure of the gp32-Dda-dT17 complex

• PDB DOI: https://doi.org/10.2210/pdb8GME/pdb
• NAKB: 8GME

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Tequatrovirus T4, Tequatrovirus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-24 Released: 2023-06-28 
• Deposition Author(s): He, X., Yun, M.K., White, S.W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.98 Å
• R-Value Free: 0.313 
• R-Value Work: 0.286 
• R-Value Observed: 0.297 

Starting Models: experimental

Literature

Crystal structure of the gp32-Dda-dT17 complex

He, X., Yun, M.K., White, S.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 181.72 kDa 
• Atom Count: 10,967 
• Modelled Residue Count: 1,346 
• Deposited Residue Count: 1,554 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gp32	A, C [auth B]	301	Tequatrovirus T4	Mutation(s): 0  Gene Names: 32
UniProt
Find proteins for P03695 (Enterobacteria phage T4) Explore P03695  Go to UniProtKB:  P03695

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dda helicase	B [auth C], D	459	Tequatrovirus	Mutation(s): 0  Gene Names: teqhal_52 EC: 5.6.2.3
UniProt
Find proteins for P32270 (Enterobacteria phage T4) Explore P32270  Go to UniProtKB:  P32270

Entity ID: 3
Molecule	Chains	Length	Organism	Image
dT17	E [auth P], F [auth Q]	17	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.98 Å
• R-Value Free: 0.313 
• R-Value Work: 0.286 
• R-Value Observed: 0.297 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.862	α = 90
b = 114.353	β = 90
c = 147.379	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-28 
Deposition Author(s): He, X., Yun, M.K., White, S.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM121293
Other private		CA021765

Revision History  

• Version 1.0: 2023-06-28
  Type: Initial release
  
• Version 2.0: 2023-11-01
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 3.0: 2023-12-20
  Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.1: 2023-12-27
  Changes: Database references, Structure summary
• Version 3.2: 2024-10-02
  Changes: Structure summary