SAXSdb — 1qqe

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

VESICULAR TRANSPORT PROTEIN SEC17

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–292	Mutation：M1I	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 5.9；277 K；POLYETHYLENEIMINE, SODIUM CITRATE, SODIUM CHLORIDE, GLYCEROL, DTT, pH 5.9, MICROBATCH, temperature 277K	Resolution 2.90 Å R-free 0.283

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 1QQE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9CRU Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 1 Deposited 2024-07-22	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 × 11 PDB declaration: undecameric	Chain G 1–292（292 aa） Chain H 1–292（292 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.89 Å
9CRX Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 3 Deposited 2024-07-22	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 × 12 PDB declaration: dodecameric	Chain G 1–292（292 aa） Chain H 1–292（292 aa） Chain I 1–292（292 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å
9N22 Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 2 Deposited 2025-01-27	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 × 12 PDB declaration: dodecameric	Chain G 1–292（292 aa） Chain H 1–292（292 aa） Chain I 1–292（292 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.91 Å
9NG2 Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 4 Deposited 2025-02-21	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 × 12 PDB declaration: dodecameric	Chain G 1–292（292 aa） Chain H 1–292（292 aa） Chain I 1–292（292 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.61 Å
9NLU Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 5 Deposited 2025-03-03	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 × 12 PDB declaration: dodecameric	Chain G 1–292（292 aa） Chain H 1–292（292 aa） Chain I 1–292（292 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.29 Å
9NLW Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 6 Deposited 2025-03-03	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 × 12 PDB declaration: dodecameric	Chain G 1–292（292 aa） Chain H 1–292（292 aa） Chain I 1–292（292 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å
9NLY Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 7 Deposited 2025-03-03	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 × 12 PDB declaration: dodecameric	Chain G 1–292（292 aa） Chain H 1–292（292 aa） Chain I 1–292（292 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.75 Å
9NLZ Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - Class 8 Deposited 2025-03-03	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 × 12 PDB declaration: dodecameric	Chain G 1–292（292 aa） Chain H 1–292（292 aa） Chain I 1–292（292 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.13 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SEC17_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–292； UniProt 1–292

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	1qqe
Deposition date deposition_date	1999-06-04
Structure title title	CRYSTAL STRUCTURE OF THE VESICULAR TRANSPORT PROTEIN SEC17
Keywords keywords	HELIX-TURN-HELIX TPR-LIKE REPEAT, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	26.32 Å
Radius of gyration Rg (electron density) rg_electron	26.18 Å
Forward intensity I(0) i0	17637600.00
Molecular weight molecular_weight	31500.0 kDa
Excluded volume excluded_volume	39200 Å³
Envelope volume envelope_volume	50031 Å³
Hydration-shell volume shell_volume	17887 Å³
Envelope diameter envelope_diameter	97.0 Å
Shell Rg shell_rg	30.31 Å
Envelope Rg envelope_rg	26.73 Å
Shape Rg shape_rg	26.16 Å
Total Rg total_rg	26.74 Å
Total atoms total_atoms	2216
Residues n_residues	281
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	90.7 Å
Rg (real space) rg_real	26.69 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	1.7640e+07
I(0) uncertainty (real space) i0_real_error	2.6320e+05
Rg (reciprocal space) rg_reciprocal	26.58 Å
I(0) (reciprocal space) i0_reciprocal	17640000.0000
Solution quality estimate total_estimate	0.7948
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.576
Kurtosis Kurtosis kurtosis	-0.357
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1578000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.682; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.416; Smooth: 0.870

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1qqea_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.8 — TPR-like
Family Family family	a.118.8.1 — Tetratricopeptide repeat (TPR)

CATH v4.4 (1 domains)

Domain ID domain_id	1qqeA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

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8. Citations (1)

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Unit-cell length a length_a	107.900 Å
Unit-cell length b length_b	107.900 Å
Unit-cell length c length_c	46.100 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	4

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	19.730 Å
R factor r_factor	0.2620
R_work r_work	0.2600
R_free r_free	0.2830

Description description	VESICULAR TRANSPORT PROTEIN SEC17
Molecular weight formula_weight	32824.7 kDa
Mutation mutation	M1I
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2220

CRYSTAL STRUCTURE OF THE VESICULAR TRANSPORT PROTEIN SEC17

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

VESICULAR TRANSPORT PROTEIN SEC17

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) 2 domains

SCOP 2.08 (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	;baker's 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	4

fit	/app/data/saxs_computation/qq/1qqe/1qqe.fit
pddf	/app/data/pr_computation/qq/1qqe/1qqe.pr.out
profile	/app/data/saxs_computation/qq/1qqe/1qqe.dat