SAXSdb — 6fg9

▼

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

VPS10 domain-containing receptor SorCS2

Mus musculus

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 116–1077 Chain B； UniProt 116–1077	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；0.1 M Sodium chloride, 0.02 M Tris pH 7.5, 0.1 M Magnesium chloride hexahydrate and 11 % w/v PEG 1500, final pH 6.4	Resolution 4.20 Å R-free 0.291

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 6FG9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6FFY Structure of the mouse SorCS2-NGF complex Deposited 2018-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 116–1077（962 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；291 K；0.225 M MES/bis-tris pH 6.6 and 6.6 % w/v PEG 6000	Resolution 3.90 Å R-free 0.305

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

View Construct and Data Evidence

UniProt name	SORC2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–963； UniProt 116–1077 Author chain B； PDBConstruct 2–963； UniProt 116–1077

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6fg9
Deposition date deposition_date	2018-01-10
Structure title title	Mouse SORCS2 ectodomain (sortilin related VPS10 domain containing receptor 2)
Keywords keywords	SorCS2, VPS10, transport, sorting, Sortilin, APOPTOSIS; APOPTOSIS
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	55.06 Å
Radius of gyration Rg (electron density) rg_electron	55.25 Å
Forward intensity I(0) i0	623656000.00
Molecular weight molecular_weight	208680.0 kDa
Excluded volume excluded_volume	261700 Å³
Envelope volume envelope_volume	422060 Å³
Hydration-shell volume shell_volume	68230 Å³
Envelope diameter envelope_diameter	186.7 Å
Shell Rg shell_rg	52.34 Å
Envelope Rg envelope_rg	53.47 Å
Shape Rg shape_rg	55.22 Å
Total Rg total_rg	55.25 Å
Total atoms total_atoms	14712
Residues n_residues	1833
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	176.0 Å
Rg (real space) rg_real	55.49 Å
Rg uncertainty (real space) rg_real_error	1.79 Å
I(0) (real space) i0_real	6.2370e+08
I(0) uncertainty (real space) i0_real_error	1.2040e+07
Rg (reciprocal space) rg_reciprocal	54.67 Å
I(0) (reciprocal space) i0_reciprocal	622900000.0000
Solution quality estimate total_estimate	0.8052
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.5 Å
Skewness Skewness skewness	0.467
Kurtosis Kurtosis kurtosis	-0.559
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	86590000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; Smooth: 0.018

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	VPS10 domain-containing receptor SorCS2
Molecular weight formula_weight	109115.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	14712

GARAVPVAGAASASRAQVSLISTSFVLKGDATHNQAMVHWTGENSSVILILTKYYHADMGKVLESSLWRSSDFGTTYTKLTLQPGVTTVIDNFYICPANKRKIILVSSSLGDREQSLFLSTDEGATFQKYPVPFLVETLLFHPKEEDKVLAYTKDSKLYVSSDLGKKWTLLQERVTKDHVFWAVSGVDDDPNLVHVEAQDLSGGYRYYTCLIYNCSAQPHIAPFSGPIDRGSLTVQDEYIFLKATSTNRTKYYVSYRRSDFVLMKLPKYALPKDLQIISTDEQQVFVAVQEWNQVDTYNLYQSDLRGVRYSLVLENVRSSRQAEENVVIDILEVRGVKGVFLANQKVDGKVTTVITYNKGRDWDYLRPPSTDMNGKPTNCQPPDCYLHLHLRWADNPYVSGTVHTKDTAPGLIMGAGNLGSQLVEYKEEMYITSDCGHTWRQVFEEEHHVLYLDHGGVIAAIKDTSIPLKILKFSVDEGHTWSTHNFTSTSVFVDGLLSEPGDETLVMTVFGHISFRSDWELVKVDFRPSFPRQCGEDDYSSWDLTDLQGDHCIMGQQRSYRKRKSTSWCVKGRSFTSALTSRVCKCRDSDFLCDYGFERSSSSESTANKCSANFWFNPLSPPEDCVLGQTYTSSLGYRKVVSNVCEGGVDLQQSPVQLQCPLQAPRGLQVSIRGEAVAVRPREDVLFVVRQEQGDVLTTKYQVDLGDGFKAMYVNLTLTGEPIRHHYESPGIYRVSVRAENMAGHDEAVLFVQVNSPLQALYLEVVPVIGVNQEVNLTAVLLPLNPNLTVFYWWIGHSLQPLLSLDNSVTTKFTDAGDVRVTVQAACGNSVLQDSRLVRVLDQFQVVPLRFSRELDTFNPNTPEWREDVGLVVTRLLSKETSIPEELLVTVVKPGLPTIADLYVLLPLPRPTRKRSLTSDKRLAAVQQALNSHRISFILRGGLRILVELRDTDTGPQRPGGSAAAHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	11

▶

8. Citations (1)

▶

Unit-cell length a length_a	138.815 Å
Unit-cell length b length_b	329.275 Å
Unit-cell length c length_c	131.409 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	4.200 Å
Low-resolution limit resolution_low	49.203 Å
R factor r_factor	0.2514
R_work r_work	0.2493
R_free r_free	0.2907

fit	/app/data/saxs_computation/fg/6fg9/6fg9.fit
pddf	/app/data/pr_computation/fg/6fg9/6fg9.pr.out
profile	/app/data/saxs_computation/fg/6fg9/6fg9.dat

Mouse SORCS2 ectodomain (sortilin related VPS10 domain containing receptor 2)

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

VPS10 domain-containing receptor SorCS2

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 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)