8IYM

Crystal structure of a protein acetyltransferase, HP0935

• PDB DOI: https://doi.org/10.2210/pdb8IYM/pdb

• Classification: TRANSFERASE
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-04-05 Released: 2024-04-10 
• Deposition Author(s): Dadireddy, V., Mahanta, P., Kumar, A., Desirazu, R.N., Ramakumar, S.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 

Literature

Crystal structure of a protein acetyltransferase, HP0935

Dadireddy, V., Mahanta, P., Kumar, A., Desirazu, R.N., Ramakumar, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56.71 kDa 
• Atom Count: 3,955 
• Modelled Residue Count: 458 
• Deposited Residue Count: 489 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyltransferase domain-containing protein	A, B, C	163	Helicobacter pylori 26695	Mutation(s): 1  Gene Names: HP_0935
UniProt
Find proteins for O25589 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25589  Go to UniProtKB:  O25589

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth A], I [auth B], P [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
SCN	G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], Q [auth C], R [auth C]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
K	D [auth A], E [auth A], O [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.856	α = 90
b = 66.17	β = 91.42
c = 70.904	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Dadireddy, V., Mahanta, P., Kumar, A., Desirazu, R.N., Ramakumar, S.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release
  
• Version 2.0: 2024-05-08
  Type: Coordinate replacement
  Reason: Real space R-factor
  Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary