SAXSdb — 9y6l

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

Avermitilol synthase

Streptomyces avermitilis

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 1–335	Mutation：A177S	DPO DIPHOSPHATE × 1 BTM N-benzyl-N,N-diethylethanaminium × 1 EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；8 mg/mL avermitilol synthase, 0.1 M bis-tris propane (pH 8.5-9.4), 30%PEG 6000, and 0.3-0.5% n-dodecyl-beta-D-maltoside	Resolution 1.29 Å R-free 0.195

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 9Y6L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Y6I Avermitilol synthase: Complex with Mg, inorganic pyrophosphate, and benzyltriethyl ammonium cation Deposited 2025-09-08	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–335（335 aa）	Not recorded	DPO DIPHOSPHATE × 1 BTM N-benzyl-N,N-diethylethanaminium × 1 EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；8 mg/mL avermitilol synthase, 0.1 M bis-tris propane (pH 8.5-9.4), 30%PEG 6000, and 0.3-0.5% n-dodecyl-beta-D-maltoside	Resolution 1.28 Å R-free 0.213
9Y6J Avermitilol synthase: Complex with Mg, inorganic pyrophosphate, and bicyclic tetralin-based tertiary amine Deposited 2025-09-08	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–335（335 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 A1CSV (2S)-N,N-dimethyl-1,2,3,4-tetrahydronaphthalen-2-amine × 1 DPO DIPHOSPHATE × 1 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；8 mg/mL avermitilol synthase, 0.1 M bis-tris propane (pH 8.5-9.4), 30%PEG 6000, and 0.3-0.5% n-dodecyl-beta-D-maltoside	Resolution 1.44 Å R-free 0.197
9Y6K Avermitilol synthase T215V: Complex with Mg, inorganic pyrophosphate, and benzyltriethyl ammonium cation Deposited 2025-09-08	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–335（335 aa）	Mutation：T215V	EDO 1,2-ETHANEDIOL × 2 BTM N-benzyl-N,N-diethylethanaminium × 1 DPO DIPHOSPHATE × 1 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；8 mg/mL avermitilol synthase, 0.1 M bis-tris propane (pH 8.5-9.4), 30%PEG 6000, and 0.3-0.5% n-dodecyl-beta-D-maltoside	Resolution 1.42 Å R-free 0.202
9Y6M Avermitilol synthase: Complex with Mg, inorganic pyrophosphate, and adamantane cation Deposited 2025-09-08	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–335（335 aa）	Not recorded	DPO DIPHOSPHATE × 1 A1CSW 1-(trimethyl-$l^{4}-azanyl)adamantane × 1 EDO 1,2-ETHANEDIOL × 2 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；8 mg/mL avermitilol synthase, 0.1 M bis-tris propane (pH 8.5-9.4), 30%PEG 6000, and 0.3-0.5% n-dodecyl-beta-D-maltoside	Resolution 1.42 Å R-free 0.201

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TPC1_STRAW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–338； UniProt 1–335

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	9y6l
Deposition date deposition_date	2025-09-08
Structure title title	Avermitilol synthase A177S: Complex with Mg, inorganic pyrophosphate, and benzyltriethyl ammonium cation
Keywords keywords	Biosynthesis, Terpene, Cyclization, LYASE; LYASE
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	19.97 Å
Radius of gyration Rg (electron density) rg_electron	18.88 Å
Forward intensity I(0) i0	23592500.00
Molecular weight molecular_weight	35712.0 kDa
Excluded volume excluded_volume	44040 Å³
Envelope volume envelope_volume	49613 Å³
Hydration-shell volume shell_volume	21535 Å³
Envelope diameter envelope_diameter	62.7 Å
Shell Rg shell_rg	25.80 Å
Envelope Rg envelope_rg	19.16 Å
Shape Rg shape_rg	18.86 Å
Total Rg total_rg	19.80 Å
Total atoms total_atoms	2511
Residues n_residues	328
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	61.9 Å
Rg (real space) rg_real	19.84 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	2.3590e+07
I(0) uncertainty (real space) i0_real_error	2.6950e+05
Rg (reciprocal space) rg_reciprocal	19.86 Å
I(0) (reciprocal space) i0_reciprocal	23590000.0000
Solution quality estimate total_estimate	0.8984
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.2 Å
Skewness Skewness skewness	0.178
Kurtosis Kurtosis kurtosis	-0.382
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7828000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.990

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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	Avermitilol synthase
Molecular weight formula_weight	36854.6 kDa
EC 编号 ec_number	4.2.3.96
Mutation mutation	A177S
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	2707

SNIMPQDIDFGLPAPAGISPGLEATRRHNLGWVRRLGLVGDGPSLAWYTSWDMPRLAACGFPHARGAALDLCADAMAFFFVFDDQFDGPLGRDPARAARVCRRLTGIVHGAGPGPGADACSAAFADVWARSTDGAHPGWVARTAHEWEYYFAAQAHEAINRLRGTPGDMESYLQVRRGISGTDLPLSLGERAAGITVPAAAFHSPQLRIMREAAIDVTLMCNDVYSLEKEEARGDMDNLVLVIEHARRCTRDEAVTAARGEVARRVIRFEQLAREVPALCAQLGLSAVERAHVDTYLGVMEAWMSGYHAWQTQTRRYTGAPHVLPSTGPGYFDEVLPT

来源 Source

来源生物 organism	Streptomyces avermitilis
NCBI Class编号 ncbi_taxonomy_id	33903
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	DIPHOSPHATE
Molecular weight formula_weight	173.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	N-benzyl-N,N-diethylethanaminium
Molecular weight formula_weight	192.3 kDa
Source method src_method	syn
Copy count entity_count	1

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	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	196

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8. Citations (1)

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Unit-cell length a length_a	95.571 Å
Unit-cell length b length_b	56.096 Å
Unit-cell length c length_c	72.693 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	125.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	1.290 Å
Low-resolution limit resolution_low	29.890 Å
R factor r_factor	0.1790
R_work r_work	0.1785
R_free r_free	0.1951

fit	/app/data/saxs_computation/y6/9y6l/9y6l.fit
pddf	/app/data/pr_computation/y6/9y6l/9y6l.pr.out
profile	/app/data/saxs_computation/y6/9y6l/9y6l.dat

Avermitilol synthase A177S: Complex with Mg, inorganic pyrophosphate, and benzyltriethyl ammonium cation

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

Avermitilol synthase

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