9ISB | pdb_00009isb

Ligand bound AGD of enzyme

• PDB DOI: https://doi.org/10.2210/pdb9ISB/pdb

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


• Deposited: 2024-07-17 Released: 2025-06-04 
• Deposition Author(s): Park, J.B., Roh, S.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.270 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Ligand bound AGD of enzyme

Park, J.B., Roh, S.H.

(2025) Proc Natl Acad Sci U S A 

• DOI: https://doi.org/10.1073/pnas.2419096122

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.

Macromolecule Content 

• Total Structure Weight: 51.89 kDa 
• Atom Count: 3,629 
• Modeled Residue Count: 458 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein acetyltransferase	A, B	234	Escherichia coli BL21(DE3)	Mutation(s): 2  Gene Names:  pat, yfiQ, ACU57_10170, BGM66_000644, BJI68_02105, C0P57_000002, CG831_000342, CIG67_15390, CTR35_002231, CV83915_03530, DTL43_02095, EIZ93_15170, FOI11_000020, FOI11_20030, FWK02_03775, G3V95_05750, G4A38_06870, G4A47_19960, GNW61_15560, GOP25_16215, GQM21_00025, GRW05_03440, HMV95_11440, J0541_000369, JNP96_20710, QDW62_06300, SAMEA3752557_00912
UniProt
Find proteins for W8T0A9 (Escherichia coli) Explore W8T0A9  Go to UniProtKB:  W8T0A9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	D [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.270 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.05	α = 90
b = 76.05	β = 90
c = 199.13	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
pointless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Park, J.B., Roh, S.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release