SAXSdb — 1b87

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

;PROTEIN (AMINOGLYCOSIDE N6'-ACETYLTRANSFERASE TYPE 1) ;

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–181	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–181	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

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 1B87	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–180（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 oligomeric state 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
2A4N Crystal structure of aminoglycoside 6'-N-acetyltransferase complexed with coenzyme A Deposited 2005-06-29	Different construct Different mutation/modification 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	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
2A4N Crystal structure of aminoglycoside 6'-N-acetyltransferase complexed with coenzyme A Deposited 2005-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–182（182 aa） Chain B 1–182（182 aa）	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
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 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 1–181； UniProt 1–181

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	1b87
Deposition date deposition_date	1999-02-09
Structure title title	CRYSTAL STRUCTURE OF AN AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE
Keywords keywords	;AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE, ANTIBIOTIC RESISTANCE, ACETYL COENZYME A, 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	18.17 Å
Radius of gyration Rg (electron density) rg_electron	16.95 Å
Forward intensity I(0) i0	8867450.00
Molecular weight molecular_weight	21377.0 kDa
Excluded volume excluded_volume	26494 Å³
Envelope volume envelope_volume	30700 Å³
Hydration-shell volume shell_volume	15461 Å³
Envelope diameter envelope_diameter	58.1 Å
Shell Rg shell_rg	22.63 Å
Envelope Rg envelope_rg	17.29 Å
Shape Rg shape_rg	16.97 Å
Total Rg total_rg	17.84 Å
Total atoms total_atoms	1503
Residues n_residues	181
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	58.1 Å
Rg (real space) rg_real	18.10 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	8.8670e+06
I(0) uncertainty (real space) i0_real_error	1.0190e+05
Rg (reciprocal space) rg_reciprocal	18.11 Å
I(0) (reciprocal space) i0_reciprocal	8867000.0000
Solution quality estimate total_estimate	0.8947
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.214
Kurtosis Kurtosis kurtosis	-0.358
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1619000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.943

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1b87a_
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 (1 domains)

Domain ID domain_id	1b87A00
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 (1)

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Unit-cell length a length_a	146.960 Å
Unit-cell length b length_b	146.960 Å
Unit-cell length c length_c	146.960 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	48

Space group space_group	I 41 3 2
Space-group number int_tables_number	214
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.1880
R_free r_free	0.2340

Description description	;PROTEIN (AMINOGLYCOSIDE N6'-ACETYLTRANSFERASE TYPE 1) ;
Molecular weight formula_weight	20602.1 kDa
Mutation mutation	VAL127GLU
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1531

CRYSTAL STRUCTURE OF AN AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE

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

;PROTEIN (AMINOGLYCOSIDE N6'-ACETYLTRANSFERASE TYPE 1) ;

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	ACETYL COENZYME *A
Molecular weight formula_weight	809.6 kDa
Source method src_method	syn
Copy count entity_count	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	28

fit	/app/data/saxs_computation/b8/1b87/1b87.fit
pddf	/app/data/pr_computation/b8/1b87/1b87.pr.out
profile	/app/data/saxs_computation/b8/1b87/1b87.dat