SAXSdb — 7sul

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

Protein transport protein Sec31A

Homo sapiens

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 1–338 Chain B； UniProt 1–338 Chain C； UniProt 1–338 Chain D； UniProt 1–338	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；30%(w/v)PEG4K,0.2M Sodium Acetat, 0.1M Tris HCL pH8.5	Resolution 2.40 Å R-free 0.237

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 7SUL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3WXA X-ray crystal structural analysis of the complex between ALG-2 and Sec31A peptide Deposited 2014-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 837–848（12 aa） Fragment：ALG-2 binding site, UNP residues 837-848	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M Cacodylate, 20% MPD, 0.05M Zinc Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.36 Å R-free 0.263
3WXA X-ray crystal structural analysis of the complex between ALG-2 and Sec31A peptide Deposited 2014-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 837–848（12 aa） Fragment：ALG-2 binding site, UNP residues 837-848	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M Cacodylate, 20% MPD, 0.05M Zinc Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.36 Å R-free 0.263

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

View Construct and Data Evidence

UniProt name	SC31A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–356； UniProt 1–338 Author chain B； PDBConstruct 19–356； UniProt 1–338 Author chain C； PDBConstruct 19–356； UniProt 1–338 Author chain D； PDBConstruct 19–356； UniProt 1–338

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	7sul
Deposition date deposition_date	2021-11-17
Structure title title	Crystal structure of the WD-repeat domain of human SEC31A
Keywords keywords	;WD-repeat, WDR, SEC31A, KIAA0905, SEC31L1, ABP125, ABP130, HSPC275, HSPC334, SGC, Structural Genomics, Structural Genomics Consortium, TRANSPORT PROTEIN ;; TRANSPORT 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	37.64 Å
Radius of gyration Rg (electron density) rg_electron	37.21 Å
Forward intensity I(0) i0	307521000.00
Molecular weight molecular_weight	141260.0 kDa
Excluded volume excluded_volume	176160 Å³
Envelope volume envelope_volume	229840 Å³
Hydration-shell volume shell_volume	51514 Å³
Envelope diameter envelope_diameter	128.2 Å
Shell Rg shell_rg	43.31 Å
Envelope Rg envelope_rg	36.46 Å
Shape Rg shape_rg	37.21 Å
Total Rg total_rg	37.57 Å
Total atoms total_atoms	9945
Residues n_residues	1330
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	123.2 Å
Rg (real space) rg_real	37.53 Å
Rg uncertainty (real space) rg_real_error	1.05 Å
I(0) (real space) i0_real	3.0750e+08
I(0) uncertainty (real space) i0_real_error	4.9800e+06
Rg (reciprocal space) rg_reciprocal	37.60 Å
I(0) (reciprocal space) i0_reciprocal	307500000.0000
Solution quality estimate total_estimate	0.8876
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	52.8 Å
Skewness Skewness skewness	0.176
Kurtosis Kurtosis kurtosis	-0.532
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	169800000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.900

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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) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7sulA01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	7sulB01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	7sulC01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	7sulD01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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8. Citations (1)

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Unit-cell length a length_a	51.180 Å
Unit-cell length b length_b	156.750 Å
Unit-cell length c length_c	85.190 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	44.370 Å
R factor r_factor	0.1900
R_work r_work	0.1890
R_free r_free	0.2370

Description description	Protein transport protein Sec31A
Molecular weight formula_weight	39378.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10025

Crystal structure of the WD-repeat domain of human SEC31A

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

Protein transport protein Sec31A

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) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	69

fit	/app/data/saxs_computation/su/7sul/7sul.fit
pddf	/app/data/pr_computation/su/7sul/7sul.pr.out
profile	/app/data/saxs_computation/su/7sul/7sul.dat