1db6

SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE

Method: SOLUTION NMR D_max: 42.9 Å Quality: GOOD

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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 1 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric	Entity 1：DNA × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	AAR ARGININEAMIDE × 1	SOLUTION NMR NMR measurement conditions：pH 6.2；293 K；Ionic strength (raw mmCIF value) 0-25 mM NaCl；Pressure ambientNMR measurement conditions：pH 6.2；278 K；Ionic strength (raw mmCIF value) 0-25 mM NaCl；Pressure ambientNMR sample composition：1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide \| 99.99% D2ONMR sample composition：1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide \| 90% H2O/10% D2O	Resolution not provided

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1db6
Deposition date deposition_date	1999-11-02
Structure title title	SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE
Keywords keywords	APTAMER, ARGININE, ARGININAMIDE, SINGLE-STRAND, HAIRPIN, SELEX, DNA; DNA
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	12.30 Å
Radius of gyration Rg (electron density) rg_electron	12.19 Å
Forward intensity I(0) i0	190639000.00
Molecular weight molecular_weight	69067.0 kDa
Excluded volume excluded_volume	67015 Å³
Envelope volume envelope_volume	12641 Å³
Hydration-shell volume shell_volume	8805 Å³
Envelope diameter envelope_diameter	44.7 Å
Shell Rg shell_rg	17.77 Å
Envelope Rg envelope_rg	13.22 Å
Shape Rg shape_rg	12.04 Å
Total Rg total_rg	12.56 Å
Total atoms total_atoms	7210
Residues n_residues	220
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	42.9 Å
Rg (real space) rg_real	12.35 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.9060e+08
I(0) uncertainty (real space) i0_real_error	2.1230e+06
Rg (reciprocal space) rg_reciprocal	12.35 Å
I(0) (reciprocal space) i0_reciprocal	190600000.0000
Solution quality estimate total_estimate	0.8561
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	12.5 Å
Skewness Skewness skewness	0.366
Kurtosis Kurtosis kurtosis	-0.515
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	148700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.747; Smooth: 0.998

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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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8. Citations (2)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	DNA
Molecular weight formula_weight	6729.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	7210

Description description	ARGININEAMIDE
Molecular weight formula_weight	174.2 kDa
Source method src_method	syn
Copy count entity_count	1

SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/db/1db6/1db6.fit
pddf	/app/data/pr_computation/db/1db6/1db6.pr.out
profile	/app/data/saxs_computation/db/1db6/1db6.dat