9Y12 | pdb_00009y12

Crystal Structure of N-Acetyl Transferase Domain-Containing Protein from Bacteroides fragilis

PDB DOI: https://doi.org/10.2210/pdb9Y12/pdb

Classification: TRANSFERASE
Organism(s): Bacteroides fragilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-29 Released: 2025-09-10
Deposition Author(s): Kim, Y., Bigelow, L., Clancy, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.224 (Depositor), 0.196 (DCC)
R-Value Work:
0.189 (Depositor), 0.193 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 9Y12

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of N-Acetyl Transferase Domain-Containing Protein from Bacteroides fragilis

Kim, Y., Bigelow, L., Clancy, L., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 154.62 kDa
Atom Count: 10,683
Modeled Residue Count: 1,216
Deposited Residue Count: 1,232
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase (GNAT) family protein	A, B, C, D, E A, B, C, D, E, F, G, H	154	Bacteroides fragilis	Mutation(s): 0 Gene Names: CQW34_04244, F2Z25_15380, F2Z89_05330
UniProt
Find proteins for Q64PL8 (Bacteroides fragilis (strain YCH46)) Explore Q64PL8 Go to UniProtKB: Q64PL8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q64PL8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain GA [auth G] SDF format, chain I [auth A] SDF format, chain JA [auth H] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth E]	CA [auth F] GA [auth G] I [auth A] JA [auth H] N [auth B] CA [auth F], GA [auth G], I [auth A], JA [auth H], N [auth B], S [auth C], U [auth D], Y [auth E]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain CA [auth F] Focus chain GA [auth G] Focus chain I [auth A] Focus chain JA [auth H] Focus chain N [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain GA [auth G] Focus chain I [auth A] Focus chain JA [auth H] Focus chain N [auth B] Focus chain S [auth C] Focus chain U [auth D] Focus chain Y [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain LA [auth H] SDF format, chain Q [auth B] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain V [auth D] SDF format, chain T [auth C] SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KA [auth H] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth G] SDF format, chain HA [auth G] SDF format, chain FA [auth F] SDF format, chain BA [auth E] SDF format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain LA [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain V [auth D] MOL2 format, chain T [auth C] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain FA [auth F] MOL2 format, chain BA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain LA [auth H] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain V [auth D] mmCIF format, chain T [auth C] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain FA [auth F] mmCIF format, chain BA [auth E] mmCIF format, chain AA [auth E]	AA [auth E] BA [auth E] DA [auth F] EA [auth F] FA [auth F] AA [auth E], BA [auth E], DA [auth F], EA [auth F], FA [auth F], HA [auth G], IA [auth G], J [auth A], K [auth A], KA [auth H], L [auth A], LA [auth H], M [auth A], P [auth B], Q [auth B], R [auth B], T [auth C], V [auth D], W [auth D], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth H] Focus chain L [auth A] Focus chain LA [auth H] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth H] Focus chain L [auth A] Focus chain LA [auth H] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain Z [auth E]	Z [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain Z [auth E] Interactions & Density Focus chain Z [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.224 (Depositor), 0.196 (DCC)
R-Value Work: 0.189 (Depositor), 0.193 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.963	α = 90
b = 92.963	β = 90
c = 218.508	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

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

Revision History (Full details and data files)

Version 1.0: 2025-09-10
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.