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9y12

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

Method: X-RAY DIFFRACTION D_max: 158.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y12
deposition_date	2025-08-29
last_revision	2025-09-10
title	Crystal Structure of N-Acetyl Transferase Domain-Containing Protein from Bacteroides fragilis
keywords	N-acetyl transferase, GNAT domain, Midwest center for Structural Genomics (MCSG), TRANSFERASE, PSI-2, Protein Structure Initiative; TRANSFERASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	49.18 Å
rg_electron	50.26 Å
i0	387563000.00
molecular_weight	152690.0 kDa
excluded_volume	186150 Å³
envelope_volume	269320 Å³
shell_volume	49367 Å³
envelope_diameter	166.1 Å
shell_rg	46.11 Å
envelope_rg	49.59 Å
shape_rg	50.24 Å
total_rg	50.14 Å
total_atoms	10620
n_residues	1192
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	158.5 Å
rg_real	50.15 Å
rg_real_error	1.98 Å
i0_real	3.8760e+08
i0_real_error	7.5500e+06
rg_reciprocal	49.19 Å
i0_reciprocal	387100000.0000
total_estimate	0.7541
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	44.6 Å
skewness	0.586
kurtosis	-0.464
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	16100000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.722; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.635; Smooth: 0.002

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Acetyltransferase (GNAT) family protein
formula_weight	18305.0 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	10683

SNAMDIISLRKSPQYLEEAIAYFQRKWADENSRMVYDNCFRTCLESESPLPQWYLLINGEGEIIGCAGLATNDFNSRMDLYPWLVALFIEEQYRGHNYGNLLIKAVEEDTRRLGFGNLYLCTTHTGYYEHFNFVYIGDCYHPWGEHTRVYQKEI

Source

organism	Bacteroides fragilis
ncbi_taxonomy_id	817
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	COENZYME A
formula_weight	767.5 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	20

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	35

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6. Citations (1)

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length_a	92.963 Å
length_b	92.963 Å
length_c	218.508 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 31
int_tables_number	144
crystal_system	trigonal

resolution	2.500 Å
resolution_low	46.480 Å
r_factor	0.1992
r_work	0.1889
r_free	0.2235

fit	/app/data/saxs_computation/y1/9y12/9y12.fit
pddf	/app/data/pr_computation/y1/9y12/9y12.pr.out
profile	/app/data/saxs_computation/y1/9y12/9y12.dat