SAXSdb — 9y12

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Acetyltransferase (GNAT) family protein

Bacteroides fragilis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–151 Chain G； UniProt 1–151	Non-standard monomer：Yes (specific site not provided by mmCIF)	COA COENZYME A × 2 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；295 K；0.2 M lithium sulfate, 0.1 M CAPS pH 10.5, 2.0 M ammonium sulfate	Resolution 2.50 Å R-free 0.224
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–151 Chain C； UniProt 1–151	Non-standard monomer：Yes (specific site not provided by mmCIF)	COA COENZYME A × 2 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；295 K；0.2 M lithium sulfate, 0.1 M CAPS pH 10.5, 2.0 M ammonium sulfate	Resolution 2.50 Å R-free 0.224
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–151 Chain E； UniProt 1–151	Non-standard monomer：Yes (specific site not provided by mmCIF)	COA COENZYME A × 2 SO4 SULFATE ION × 5 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；295 K；0.2 M lithium sulfate, 0.1 M CAPS pH 10.5, 2.0 M ammonium sulfate	Resolution 2.50 Å R-free 0.224
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 1–151 Chain H； UniProt 1–151	Non-standard monomer：Yes (specific site not provided by mmCIF)	COA COENZYME A × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 10.5；295 K；0.2 M lithium sulfate, 0.1 M CAPS pH 10.5, 2.0 M ammonium sulfate	Resolution 2.50 Å R-free 0.224

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A149N1Y8_BACFG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–154； UniProt 1–151 Author chain B； PDBConstruct 4–154； UniProt 1–151 Author chain C； PDBConstruct 4–154； UniProt 1–151 Author chain D； PDBConstruct 4–154； UniProt 1–151 Author chain E； PDBConstruct 4–154； UniProt 1–151 Author chain F； PDBConstruct 4–154； UniProt 1–151 Author chain G； PDBConstruct 4–154； UniProt 1–151 Author chain H； PDBConstruct 4–154； UniProt 1–151

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

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

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	49.18 Å
Radius of gyration Rg (electron density) rg_electron	50.26 Å
Forward intensity I(0) i0	387563000.00
Molecular weight molecular_weight	152690.0 kDa
Excluded volume excluded_volume	186150 Å³
Envelope volume envelope_volume	269320 Å³
Hydration-shell volume shell_volume	49367 Å³
Envelope diameter envelope_diameter	166.1 Å
Shell Rg shell_rg	46.11 Å
Envelope Rg envelope_rg	49.59 Å
Shape Rg shape_rg	50.24 Å
Total Rg total_rg	50.14 Å
Total atoms total_atoms	10620
Residues n_residues	1192
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	158.5 Å
Rg (real space) rg_real	50.15 Å
Rg uncertainty (real space) rg_real_error	1.98 Å
I(0) (real space) i0_real	3.8760e+08
I(0) uncertainty (real space) i0_real_error	7.5500e+06
Rg (reciprocal space) rg_reciprocal	49.19 Å
I(0) (reciprocal space) i0_reciprocal	387100000.0000
Solution quality estimate total_estimate	0.7541
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.6 Å
Skewness Skewness skewness	0.586
Kurtosis Kurtosis kurtosis	-0.464
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16100000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Acetyltransferase (GNAT) family protein
Molecular weight formula_weight	18305.0 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	10683

SNAMDIISLRKSPQYLEEAIAYFQRKWADENSRMVYDNCFRTCLESESPLPQWYLLINGEGEIIGCAGLATNDFNSRMDLYPWLVALFIEEQYRGHNYGNLLIKAVEEDTRRLGFGNLYLCTTHTGYYEHFNFVYIGDCYHPWGEHTRVYQKEI

来源 Source

来源生物 organism	Bacteroides fragilis
NCBI Class编号 ncbi_taxonomy_id	817
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

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8. Citations (1)

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Unit-cell length a length_a	92.963 Å
Unit-cell length b length_b	92.963 Å
Unit-cell length c length_c	218.508 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	trigonal

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	46.480 Å
R factor r_factor	0.1992
R_work r_work	0.1889
R_free 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

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Acetyltransferase (GNAT) family protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction