SAXSdb — 9yaa

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

SnoaL-like domain-containing protein

Mycobacterium ulcerans Agy99

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 2–124	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.2；291 K；12% 4000, 0.1M sodium acetate pH 4.2, 10mM dihdrogen potassium phosphate. MyulA.17060.a.A1.PB00143 at 15 mg/mL. Liu-S-182 drop CD/4, Puck: PSL-0407, Cryo: 32% PEG 4000, 0.2M sodium acetate pH 4.0	Resolution 1.36 Å R-free 0.181

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 9YAA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
12IS Crystal structure of a SnoaL-like domain-containing protein from Mycobacterium ulcerans (Zinc Bound) Deposited 2026-04-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–124（123 aa） Fragment：S2-Y125	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2 ZN ZINC ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；291 K；12% 4000, 0.1M sodium acetate pH 4.2, 10mM dihdrogen potassium phosphate. MyulA.17060.a.A1.PB00143 at 15 mg/mL. Liu-S-182 drop CD/4, Puck: PSL-0405, Cryo: 32% PEG 4000, 0.2M sodium acetate pH 4.0	Resolution 1.31 Å R-free 0.174
9PL2 Crystal structure of a SnoaL-like domain-containing protein from Mycobacterium ulcerans Deposited 2025-07-15	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 2–124（123 aa） Chain B 2–124（123 aa）	Not recorded	PO4 PHOSPHATE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.8；291 K；8% (w/v) PEG 4K, 0.1M Cit pH 3.8, 10mM potassium dihydrogen phosphate. MyulA.17060.a.A1.PB00143 at 15 mg/mL. plate Liu-S-182 C1 Puck: PSL0114, Cryo: 75% crystallant + 25% PEG 200.	Resolution 1.37 Å R-free 0.190

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0PR67_MYCUA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–146； UniProt 2–124

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	9yaa
Deposition date deposition_date	2025-09-15
最后修订 last_revision	2025-09-24
Structure title title	Crystal structure of a SnoaL-like domain-containing protein from Mycobacterium ulcerans (Orthorhombic C form)
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, SnoaL-like domain, ISOMERASE; ISOMERASE
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	15.31 Å
Radius of gyration Rg (electron density) rg_electron	13.81 Å
Forward intensity I(0) i0	3975850.00
Molecular weight molecular_weight	14177.0 kDa
Excluded volume excluded_volume	17786 Å³
Envelope volume envelope_volume	19840 Å³
Hydration-shell volume shell_volume	12229 Å³
Envelope diameter envelope_diameter	49.4 Å
Shell Rg shell_rg	19.57 Å
Envelope Rg envelope_rg	14.08 Å
Shape Rg shape_rg	13.79 Å
Total Rg total_rg	15.09 Å
Total atoms total_atoms	1001
Residues n_residues	119
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	49.5 Å
Rg (real space) rg_real	15.18 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	3.9760e+06
I(0) uncertainty (real space) i0_real_error	4.4040e+04
Rg (reciprocal space) rg_reciprocal	15.19 Å
I(0) (reciprocal space) i0_reciprocal	3976000.0000
Solution quality estimate total_estimate	0.8742
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	0.076
Kurtosis Kurtosis kurtosis	-0.326
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	833400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.970

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	SnoaL-like domain-containing protein
Molecular weight formula_weight	16936.1 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	1170

MAHHHHHHMGTLEAQTQGPGSMVSIALLREMFEKMVVAKNAELIGHYYDPDFVMYSDGLRQEFAEFNEGHRKIYASAISYAIEYDEDAWVQAPDRVAGRVWITTSRPGEKPTRIEVILIAAYRDCRIHRIWETTWPSWRNVAALED

来源 Source

来源生物 organism	Mycobacterium ulcerans Agy99
NCBI Class编号 ncbi_taxonomy_id	362242
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	114

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8. Citations (1)

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Unit-cell length a length_a	62.073 Å
Unit-cell length b length_b	71.564 Å
Unit-cell length c length_c	56.445 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 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.360 Å
Low-resolution limit resolution_low	46.890 Å
R factor r_factor	0.1591
R_work r_work	0.1579
R_free r_free	0.1815

fit	/app/data/saxs_computation/ya/9yaa/9yaa.fit
pddf	/app/data/pr_computation/ya/9yaa/9yaa.pr.out
profile	/app/data/saxs_computation/ya/9yaa/9yaa.dat

Crystal structure of a SnoaL-like domain-containing protein from Mycobacterium ulcerans (Orthorhombic C form)

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

SnoaL-like domain-containing protein

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