SAXSdb — 9ydf

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

Solute carrier family 9 member C1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 859–1013	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；20% (w/v) polyethylene glycol (PEG) 3350, 0.2 M Calcium chloride dihydrate	Resolution 2.18 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	SL9C1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–173； UniProt 859–1013

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	9ydf
Deposition date deposition_date	2025-09-22
最后修订 last_revision	2025-11-12
Structure title title	Structure of the cyclic nucleotide binding domain of SLC9C1
Keywords keywords	;Transporter, cyclic nucleotide binding domain, sperm-specific protein, SGC, TRANSPORT PROTEIN, Structural Genomics, PSI-2, Protein Structure Initiative, Structural Genomics Consortium ;; 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	15.71 Å
Radius of gyration Rg (electron density) rg_electron	14.31 Å
Forward intensity I(0) i0	3788760.00
Molecular weight molecular_weight	14494.0 kDa
Excluded volume excluded_volume	18445 Å³
Envelope volume envelope_volume	20682 Å³
Hydration-shell volume shell_volume	12379 Å³
Envelope diameter envelope_diameter	45.9 Å
Shell Rg shell_rg	19.87 Å
Envelope Rg envelope_rg	14.49 Å
Shape Rg shape_rg	14.31 Å
Total Rg total_rg	15.50 Å
Total atoms total_atoms	1017
Residues n_residues	131
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	47.5 Å
Rg (real space) rg_real	15.60 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	3.7890e+06
I(0) uncertainty (real space) i0_real_error	3.8670e+04
Rg (reciprocal space) rg_reciprocal	15.61 Å
I(0) (reciprocal space) i0_reciprocal	3789000.0000
Solution quality estimate total_estimate	0.9091
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	46.9 Å
Skewness Skewness skewness	0.056
Kurtosis Kurtosis kurtosis	-0.500
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	388300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.979

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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	Solute carrier family 9 member C1
Molecular weight formula_weight	19986.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1043

MHHHHHHSSGRENLYFQGPLTVEEVLYHIPWLDKNKDYINFIQEKAKVVTFDCGNDIFEEGDEPKGIYIIISGMVKLEKSKPGLGIDQMVESKEKDFPIIDTDYMLSGEIIGEINCLTNEPMKYSATCKTVVETCFIPKTHLYDAFEQCSPLIKQKMWLKLGLAITARKIREH

来源 Source

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	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

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8. Citations (1)

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Unit-cell length a length_a	45.788 Å
Unit-cell length b length_b	45.788 Å
Unit-cell length c length_c	276.932 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 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.180 Å
Low-resolution limit resolution_low	46.160 Å
R factor r_factor	0.2042
R_work r_work	0.2026
R_free r_free	0.2374

fit	/app/data/saxs_computation/yd/9ydf/9ydf.fit
pddf	/app/data/pr_computation/yd/9ydf/9ydf.pr.out
profile	/app/data/saxs_computation/yd/9ydf/9ydf.dat

Structure of the cyclic nucleotide binding domain of SLC9C1

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

Solute carrier family 9 member C1

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