SAXSdb — 2a4n

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

aac(6')-Ii

Enterococcus faecium

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 1–182 Chain B； UniProt 1–182	Not recorded	COA COENZYME A × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；HEPES, EDTA, coenzyme A, 2-(6'-N-sisomycin)acetic acid, tri-sodium citrate, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.255
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–182 Chain B； UniProt 1–182	Not recorded	COA COENZYME A × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；HEPES, EDTA, coenzyme A, 2-(6'-N-sisomycin)acetic acid, tri-sodium citrate, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.255

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.

Other PDB	Difference from Current Entry 2A4N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B87 CRYSTAL STRUCTURE OF AN AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE Deposited 1999-02-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–181（181 aa）	Mutation：VAL127GLU	ACO ACETYL COENZYME *A × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.70 Å R-free 0.234
1B87 CRYSTAL STRUCTURE OF AN AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE Deposited 1999-02-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–181（181 aa）	Mutation：VAL127GLU	ACO ACETYL COENZYME *A × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.70 Å R-free 0.234
1N71 Crystal structure of aminoglycoside 6'-acetyltransferase type Ii in complex with coenzyme A Deposited 2002-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–180（180 aa） Chain B 1–180（180 aa）	Not recorded	COA COENZYME A × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.80 Å R-free 0.245
1N71 Crystal structure of aminoglycoside 6'-acetyltransferase type Ii in complex with coenzyme A Deposited 2002-11-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–180（180 aa） Chain D 1–180（180 aa）	Not recorded	COA COENZYME A × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.80 Å R-free 0.245
1N71 Crystal structure of aminoglycoside 6'-acetyltransferase type Ii in complex with coenzyme A Deposited 2002-11-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–180（180 aa） Chain B 1–180（180 aa） Chain C 1–180（180 aa） Chain D 1–180（180 aa）	Not recorded	COA COENZYME A × 4 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.80 Å R-free 0.245
7BXZ Crystal structure of the aminoglycoside 6'-N-acetyltransferase from Enterococcus faecium Deposited 2020-04-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–182（182 aa） Chain B 1–182（182 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM HEPES-Na (pH 7.0), 10 mM magnesium chloride, 1.6 M ammonium sulfate	Resolution 2.50 Å R-free 0.265
7BXZ Crystal structure of the aminoglycoside 6'-N-acetyltransferase from Enterococcus faecium Deposited 2020-04-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–182（182 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM HEPES-Na (pH 7.0), 10 mM magnesium chloride, 1.6 M ammonium sulfate	Resolution 2.50 Å R-free 0.265

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q47764_ENTFC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–182； UniProt 1–182 Author chain B； PDBConstruct 1–182； UniProt 1–182

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	2a4n
Deposition date deposition_date	2005-06-29
Structure title title	Crystal structure of aminoglycoside 6'-N-acetyltransferase complexed with coenzyme A
Keywords keywords	alpha beta protein, N-acetyl transferase, TRANSFERASE; 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	22.40 Å
Radius of gyration Rg (electron density) rg_electron	21.13 Å
Forward intensity I(0) i0	32361400.00
Molecular weight molecular_weight	42539.0 kDa
Excluded volume excluded_volume	52660 Å³
Envelope volume envelope_volume	61603 Å³
Hydration-shell volume shell_volume	24169 Å³
Envelope diameter envelope_diameter	76.0 Å
Shell Rg shell_rg	27.98 Å
Envelope Rg envelope_rg	21.13 Å
Shape Rg shape_rg	21.07 Å
Total Rg total_rg	22.11 Å
Total atoms total_atoms	2988
Residues n_residues	359
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	72.3 Å
Rg (real space) rg_real	22.29 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	3.2360e+07
I(0) uncertainty (real space) i0_real_error	4.3040e+05
Rg (reciprocal space) rg_reciprocal	22.32 Å
I(0) (reciprocal space) i0_reciprocal	32360000.0000
Solution quality estimate total_estimate	0.7386
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.198
Kurtosis Kurtosis kurtosis	-0.385
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5057000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 0.328; Positv: 1.000; Valcen: 0.995; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	aac(6')-Ii
Molecular weight formula_weight	20730.2 kDa
EC 编号 ec_number	2.3.1.82
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3186

MIISEFDRNNPVLKDQLSDLLRLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGITIYLGTDDLDHGTTLSQTDLYEHTFDKVASIQNLREHPYEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRPDSQ

来源 Source

来源生物 organism	Enterococcus faecium
NCBI Class编号 ncbi_taxonomy_id	1352
宿主生物 host_organism	Escherichia coli str. K12 substr. W3110

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	2

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	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	198

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2a4na_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

Domain ID domain_id	d2a4nb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

CATH v4.4 (2 domains)

Domain ID domain_id	2a4nA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	2a4nB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

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8. Citations (3)

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Unit-cell length a length_a	71.480 Å
Unit-cell length b length_b	127.350 Å
Unit-cell length c length_c	76.910 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	48.430 Å
R factor r_factor	0.2060
R_work r_work	0.2060
R_free r_free	0.2550

fit	/app/data/saxs_computation/a4/2a4n/2a4n.fit
pddf	/app/data/pr_computation/a4/2a4n/2a4n.pr.out
profile	/app/data/saxs_computation/a4/2a4n/2a4n.dat

Crystal structure of aminoglycoside 6'-N-acetyltransferase complexed with coenzyme A

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

aac(6')-Ii

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