SAXSdb — 6bvc

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

Aminoglycoside-(3)-N-acetyltransferase

Serratia marcescens

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 1–177	Not recorded	COA COENZYME A × 2 CL CHLORIDE ION × 2 PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 4 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；0.2M NaCl, 25% PEG3350, 0.1M Na Citrate pH5.6, cryo paratone	Resolution 1.81 Å R-free 0.191

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 6BVC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BO4 CRYSTAL STRUCTURE OF A GCN5-RELATED N-ACETYLTRANSFERASE: SERRATIA MARESCENS AMINOGLYCOSIDE 3-N-ACETYLTRANSFERASE Deposited 1998-08-08	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 1–168（168 aa） Chain B 1–168（168 aa）	Not recorded	SPD SPERMIDINE × 1 COA COENZYME A × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；277 K；SITTING DROP, 4 DEGREES C, 3.5MG/ML PROTEIN + 5MM COA, 100MM TRIS-HCL PH7.8, 0.8% PEG4K, 18% T-BUTANOL, 20MM SRCL2, 7% DIOXANE, 5% 2,4-METHYLPENTANEDIOL, 40MM HEXANEDIOL, 10MM DITHIOTHREITOL, 2MM TRIS(2-CARBOXY- ETHYL)PHOSPHINE-HCL, 10MM SPERMIDINE, 2.5% GLYCEROL, vapor diffusion - sitting drop, temperature 277K	Resolution 2.30 Å R-free 0.250

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q53396_SERMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–177； UniProt 1–177

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	6bvc
Deposition date deposition_date	2017-12-12
Structure title title	Crystal structure of AAC(3)-Ia in complex with coenzyme A
Keywords keywords	;aminoglycoside, antibiotic, resistance, GCN5 family N-acetyltransferase, GNAT, alpha/beta protein, coenzyme A, CoA, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, 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	17.74 Å
Radius of gyration Rg (electron density) rg_electron	16.33 Å
Forward intensity I(0) i0	6666840.00
Molecular weight molecular_weight	18321.0 kDa
Excluded volume excluded_volume	22783 Å³
Envelope volume envelope_volume	28374 Å³
Hydration-shell volume shell_volume	14822 Å³
Envelope diameter envelope_diameter	62.6 Å
Shell Rg shell_rg	22.19 Å
Envelope Rg envelope_rg	16.78 Å
Shape Rg shape_rg	16.31 Å
Total Rg total_rg	17.44 Å
Total atoms total_atoms	1284
Residues n_residues	154
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	61.7 Å
Rg (real space) rg_real	17.64 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	6.6670e+06
I(0) uncertainty (real space) i0_real_error	7.9580e+04
Rg (reciprocal space) rg_reciprocal	17.65 Å
I(0) (reciprocal space) i0_reciprocal	6667000.0000
Solution quality estimate total_estimate	0.7816
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.159
Kurtosis Kurtosis kurtosis	-0.252
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	962200.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.725; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000

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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	Aminoglycoside-(3)-N-acetyltransferase
Molecular weight formula_weight	19436.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1498

MLRSSNDVTQQGSRPKTKLGGSSMGIIRTCRLGPDQVKSMRAALDLFGREFGDVATYSQHQPDSDYLGNLLRSKTFIALAAFDQEAVVGALAAYVLPKFEQPRSEIYIYDLAVSGEHRRQGIATALINLLKHEANALGAYVIYVQADYGDDPAVALYTKLGIREEVMHFDIDPSTAT

来源 Source

来源生物 organism	Serratia marcescens
NCBI Class编号 ncbi_taxonomy_id	615
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	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
Molecular weight formula_weight	634.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	184

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6bvca_
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.108.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	6bvcA00
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	79.028 Å
Unit-cell length b length_b	100.875 Å
Unit-cell length c length_c	53.031 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	8

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

Resolution resolution	1.808 Å
Low-resolution limit resolution_low	50.438 Å
R factor r_factor	0.1637
R_work r_work	0.1623
R_free r_free	0.1914

fit	/app/data/saxs_computation/bv/6bvc/6bvc.fit
pddf	/app/data/pr_computation/bv/6bvc/6bvc.pr.out
profile	/app/data/saxs_computation/bv/6bvc/6bvc.dat

Crystal structure of AAC(3)-Ia in complex with coenzyme A