SAXSdb — 9y5g

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：rv-SNARE/sc-t × 1 Entity 2：sc-t-SNARE-5.s.8 × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Succinic acid pH 7.0 and 15% (w/v) PEG 3350	Resolution 2.10 Å R-free 0.278
2	Protein heterocomplex Heteromer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：rv-SNARE/sc-t × 1 Entity 2：sc-t-SNARE-5.s.8 × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Succinic acid pH 7.0 and 15% (w/v) PEG 3350	Resolution 2.10 Å R-free 0.278

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	9y5g
Deposition date deposition_date	2025-09-04
Structure title title	Crystal Structure of rv-SNARE/sc-t-SNARE-5.s.8 complex
Keywords keywords	membrane fusion proteins, synthetic fusogens, SNARE, protein design, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	36.43 Å
Radius of gyration Rg (electron density) rg_electron	37.28 Å
Forward intensity I(0) i0	88031700.00
Molecular weight molecular_weight	71395.0 kDa
Excluded volume excluded_volume	88202 Å³
Envelope volume envelope_volume	120700 Å³
Hydration-shell volume shell_volume	30186 Å³
Envelope diameter envelope_diameter	153.2 Å
Shell Rg shell_rg	37.56 Å
Envelope Rg envelope_rg	38.50 Å
Shape Rg shape_rg	37.35 Å
Total Rg total_rg	37.07 Å
Total atoms total_atoms	4994
Residues n_residues	598
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	147.1 Å
Rg (real space) rg_real	37.13 Å
Rg uncertainty (real space) rg_real_error	2.42 Å
I(0) (real space) i0_real	8.8030e+07
I(0) uncertainty (real space) i0_real_error	1.8270e+06
Rg (reciprocal space) rg_reciprocal	36.70 Å
I(0) (reciprocal space) i0_reciprocal	87990000.0000
Solution quality estimate total_estimate	0.7094
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.6 Å
Skewness Skewness skewness	0.749
Kurtosis Kurtosis kurtosis	0.201
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5178000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.369; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.175; Smooth: 0.937

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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	rv-SNARE/sc-t
Molecular weight formula_weight	8671.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	5302

MSSSSNEKLRETLREVEDVKNIMEDNRRLVERQGRQIDRLEEKADDLERSAERLSDNSEKLKRKYWWKNSK

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	sc-t-SNARE-5.s.8
Molecular weight formula_weight	28983.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

SGGSSSEREKEIDEGLDRVSEIVKELKKMAEEMRRMIEEQGRRIERIEEKAEEAKEKIEEANERAEKLLKDPGGSGGSEELKKLEKEGEKLKELVEELDREIKELKEGMERLREMFEEAAKLSEEALEIMRRTRKLSEEELEEAKQKAKEQEKEKALKEKGGSGGSGGSEKVKRELAQIEERHQQILELEEKIKELLEMFKELSEKIEEQGQKIDRIEDKVSKAKEHVEKGVEDTKKAVKYQSKARRKK

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	302

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8. Citations (1)

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Unit-cell length a length_a	43.182 Å
Unit-cell length b length_b	45.704 Å
Unit-cell length c length_c	341.124 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	33.340 Å
R factor r_factor	0.2298
R_work r_work	0.2274
R_free r_free	0.2781

fit	/app/data/saxs_computation/y5/9y5g/9y5g.fit
pddf	/app/data/pr_computation/y5/9y5g/9y5g.pr.out
profile	/app/data/saxs_computation/y5/9y5g/9y5g.dat

Crystal Structure of rv-SNARE/sc-t-SNARE-5.s.8 complex

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

Assembly Composition of the Current Entry

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)