SAXSdb — 3lgo

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

Protein SLM4

Saccharomyces cerevisiae

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–162	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3；293 K；100 mM sodium citrate buffer, pH 2.0, 500-800 mM ammonium sulfate, 200 mM lithium sulfate, 200-350 mM L-arginine-HCl, pH 5.75, 5% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.85 Å R-free 0.351
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–162	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3；293 K；100 mM sodium citrate buffer, pH 2.0, 500-800 mM ammonium sulfate, 200 mM lithium sulfate, 200-350 mM L-arginine-HCl, pH 5.75, 5% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.85 Å R-free 0.351

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 3LGO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4FTX Crystal structure of Ego3 homodimer Deposited 2012-06-28	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 1–162（162 aa） Chain B 1–162（162 aa）	Not recorded	SIN SUCCINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；35% tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.10 Å R-free 0.221
4FUW Crystal structure of Ego3 mutant Deposited 2012-06-28	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 1–162（162 aa） Chain B 1–162（162 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6M ammonium sulfate, 0.1M MES monohydrate, 10% 1,4-dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.253
4XPM Crystal structure of EGO-TC Deposited 2015-01-17	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–162（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.2M NaCl, 0.1M Bis-Tris (pH 5.5), 25% PEG 3350	Resolution 2.40 Å R-free 0.217
6JWP crystal structure of EGOC Deposited 2019-04-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–162（162 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000	Resolution 3.20 Å R-free 0.285
6JWP crystal structure of EGOC Deposited 2019-04-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 1–162（162 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000	Resolution 3.20 Å R-free 0.285
9H4Q Cryo-EM structure of the SEAC wing - EGOC Deposited 2024-10-21	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain Y 1–162（162 aa）	Not recorded	MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain Y 1–162（162 aa） Chain Z 1–162（162 aa）	Not recorded	ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SLM4_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–172； UniProt 1–162

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	3lgo
Deposition date deposition_date	2010-01-21
Structure title title	Structure of Gse1p, member of the GSE/EGO complex
Keywords keywords	Roadblock/LC7, domain swap, Autophagy, Membrane, Transmembrane, Transport, Vacuole, Protein binding; PROTEIN BINDING
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	20.65 Å
Radius of gyration Rg (electron density) rg_electron	20.63 Å
Forward intensity I(0) i0	4615120.00
Molecular weight molecular_weight	15560.0 kDa
Excluded volume excluded_volume	19523 Å³
Envelope volume envelope_volume	26963 Å³
Hydration-shell volume shell_volume	12874 Å³
Envelope diameter envelope_diameter	79.9 Å
Shell Rg shell_rg	23.50 Å
Envelope Rg envelope_rg	22.74 Å
Shape Rg shape_rg	20.65 Å
Total Rg total_rg	21.09 Å
Total atoms total_atoms	1092
Residues n_residues	140
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	79.5 Å
Rg (real space) rg_real	21.21 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	4.6150e+06
I(0) uncertainty (real space) i0_real_error	7.0600e+04
Rg (reciprocal space) rg_reciprocal	21.11 Å
I(0) (reciprocal space) i0_reciprocal	4615000.0000
Solution quality estimate total_estimate	0.6795
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	19.6 Å
Skewness Skewness skewness	0.926
Kurtosis Kurtosis kurtosis	0.337
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	709000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.209; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.209; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3lgoA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	30 — Dynein light chain 2a, cytoplasmic

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8. Citations (1)

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Unit-cell length a length_a	73.290 Å
Unit-cell length b length_b	73.290 Å
Unit-cell length c length_c	147.280 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.3170
R_free r_free	0.3510

Description description	Protein SLM4
Molecular weight formula_weight	19563.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1094

Structure of Gse1p, member of the GSE/EGO complex

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

Protein SLM4

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

fit	/app/data/saxs_computation/lg/3lgo/3lgo.fit
pddf	/app/data/pr_computation/lg/3lgo/3lgo.pr.out
profile	/app/data/saxs_computation/lg/3lgo/3lgo.dat