SAXSdb — 12cj

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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	Nucleic acid only No protein 蛋白 0 / DNA 0 / RNA 1 / 其他Polymer 0 PDB declaration: monomeric	Entity 1：DGR-1B × 1 缺少 UniProt 身份时不显示参考序列区间	Non-standard monomer：Yes (specific site not provided by mmCIF)	SR STRONTIUM ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；10% v/v MPD, 20 mM spermine, 50 mM strontium chloride, 50 mM lithium chloride, 40 mM sodium cacodylate	Resolution 2.93 Å R-free 0.248
2	Nucleic acid only No protein 蛋白 0 / DNA 0 / RNA 1 / 其他Polymer 0 PDB declaration: monomeric	Entity 1：DGR-1B × 1 缺少 UniProt 身份时不显示参考序列区间	Non-standard monomer：Yes (specific site not provided by mmCIF)	SR STRONTIUM ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；10% v/v MPD, 20 mM spermine, 50 mM strontium chloride, 50 mM lithium chloride, 40 mM sodium cacodylate	Resolution 2.93 Å R-free 0.248

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	12cj
Deposition date deposition_date	2026-03-26
最后修订 last_revision	2026-05-13
Structure title title	Apo structure of dopamine-binding aptamer, DGR-1B
Keywords keywords	riboswitch, aptamer, dopamine, SELEX, L-DOPA, RNA; RNA
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	33.93 Å
Radius of gyration Rg (electron density) rg_electron	34.19 Å
Forward intensity I(0) i0	128821000.00
Molecular weight molecular_weight	52554.0 kDa
Excluded volume excluded_volume	48409 Å³
Envelope volume envelope_volume	79577 Å³
Hydration-shell volume shell_volume	21713 Å³
Envelope diameter envelope_diameter	112.5 Å
Shell Rg shell_rg	36.07 Å
Envelope Rg envelope_rg	33.62 Å
Shape Rg shape_rg	34.13 Å
Total Rg total_rg	34.35 Å
Total atoms total_atoms	3331
Residues n_residues	152
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	107.0 Å
Rg (real space) rg_real	34.33 Å
Rg uncertainty (real space) rg_real_error	1.04 Å
I(0) (real space) i0_real	1.2880e+08
I(0) uncertainty (real space) i0_real_error	2.4190e+06
Rg (reciprocal space) rg_reciprocal	34.09 Å
I(0) (reciprocal space) i0_reciprocal	128800000.0000
Solution quality estimate total_estimate	0.7174
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.8 Å
Skewness Skewness skewness	0.466
Kurtosis Kurtosis kurtosis	-0.754
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3693000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.640; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.294; Smooth: 0.109

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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	DGR-1B
Molecular weight formula_weight	24954.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A,B
Atom count atom_count	3349

GGACUAGACUCCGUAAUUCGCGUGGAUAUGGCACGCAGUAAGGUAUUGGGCACCGUAAAUGUCCAUAUGUUAGUCCA

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	STRONTIUM ION
Molecular weight formula_weight	87.6 kDa
Source method src_method	nat
Copy count entity_count	27

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	18

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8. Citations (1)

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Unit-cell length a length_a	162.764 Å
Unit-cell length b length_b	35.927 Å
Unit-cell length c length_c	97.279 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	120.64 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.930 Å
Low-resolution limit resolution_low	43.830 Å
R factor r_factor	0.2036
R_work r_work	0.2015
R_free r_free	0.2480

fit	/app/data/saxs_computation/2c/12cj/12cj.fit
pddf	/app/data/pr_computation/2c/12cj/12cj.pr.out
profile	/app/data/saxs_computation/2c/12cj/12cj.dat

Apo structure of dopamine-binding aptamer, DGR-1B

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