SAXSdb — 1n71

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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 1–180 Chain B； UniProt 1–180	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–180 Chain D； UniProt 1–180	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
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–180 Chain B； UniProt 1–180 Chain C； UniProt 1–180 Chain D； UniProt 1–180	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

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 1N71	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
2A4N Crystal structure of aminoglycoside 6'-N-acetyltransferase complexed with coenzyme A Deposited 2005-06-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–182（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 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 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 6 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 1–180； UniProt 1–180 Author chain B； PDBConstruct 1–180； UniProt 1–180 Author chain C； PDBConstruct 1–180； UniProt 1–180 Author chain D； PDBConstruct 1–180； UniProt 1–180

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	1n71
Deposition date deposition_date	2002-11-12
Structure title title	Crystal structure of aminoglycoside 6'-acetyltransferase type Ii in complex with coenzyme A
Keywords keywords	;AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE, ANTIBIOTIC RESISTANCE, 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	33.70 Å
Radius of gyration Rg (electron density) rg_electron	33.33 Å
Forward intensity I(0) i0	121065000.00
Molecular weight molecular_weight	85208.0 kDa
Excluded volume excluded_volume	105410 Å³
Envelope volume envelope_volume	134050 Å³
Hydration-shell volume shell_volume	35731 Å³
Envelope diameter envelope_diameter	117.3 Å
Shell Rg shell_rg	37.63 Å
Envelope Rg envelope_rg	33.11 Å
Shape Rg shape_rg	33.29 Å
Total Rg total_rg	33.79 Å
Total atoms total_atoms	5983
Residues n_residues	718
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	111.9 Å
Rg (real space) rg_real	33.96 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	1.2110e+08
I(0) uncertainty (real space) i0_real_error	1.8510e+06
Rg (reciprocal space) rg_reciprocal	33.80 Å
I(0) (reciprocal space) i0_reciprocal	121000000.0000
Solution quality estimate total_estimate	0.8184
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	31.0 Å
Skewness Skewness skewness	0.561
Kurtosis Kurtosis kurtosis	-0.325
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22070000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.757; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.802; Smooth: 0.562

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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	20515.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6487

MIISEFDRNNPVLKDQLSDLLRLTWPEEYGDSSAEEVEEMMNPERIAVAAVDQDELVGFIGAIPQYGITGWELHPLVVESSRRKNQIGTRLVNYLEKEVASRGGITIYLGTDDLDHGTTLSQTDLYEHTFDKVASIQNLREHPYEFYEKLGYKIVGVLPNANGWDKPDIWMAKTIIPRPD

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

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	4

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	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	504

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1n71a_
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	d1n71b_
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	d1n71c_
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	d1n71d_
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 (4 domains)

Domain ID domain_id	1n71A00
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	1n71B00
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	1n71C00
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	1n71D00
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 (2)

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Unit-cell length a length_a	73.190 Å
Unit-cell length b length_b	76.920 Å
Unit-cell length c length_c	130.150 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	27.970 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2450

fit	/app/data/saxs_computation/n7/1n71/1n71.fit
pddf	/app/data/pr_computation/n7/1n71/1n71.pr.out
profile	/app/data/saxs_computation/n7/1n71/1n71.dat

Crystal structure of aminoglycoside 6'-acetyltransferase type Ii in complex 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