9y74

[22L-7B C|A] 22 bp L-DNA tensegrity triangle that propagates via blunt-end stacking with C stacking on A at the interface

Method: X-RAY DIFFRACTION D_max: 76.2 Å Quality: REASONABLE

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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 12 / RNA 0 / 其他Polymer 0 PDB declaration: dodecameric	Entity 1：;DNA (5'-D((0DC)P(0DG)P(0DA)P(0DT)P(0DG)P(0DC)P(0DC)P(0DT)P(0DG)P(0DT)P(0DA)P(0DC)P(0DG)(0DG)P(0DA)P(0DC)P(0DA)P(0DG)P(0DA)P(0DT)P(0DC)P(0DA))-3') ; × 3 Entity 2：;DNA (5'-D(P(0DC)P(0DC)P(0DG)P(0DT)P(0DA)P(0DC)P(0DA))-3') ; × 3 Entity 3：;DNA (5'-D(P(0DG)P(0DG)P(0DC)P(0DA)P(0DT)P(0DC)P(0DG))-3') ; × 3 Entity 4：;DNA (5'-D((0DT)P(0DG)P(0DA)P(0DT)P(0DC)P(0DT)P(0DG)P*(0DT))-3') ; × 3 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) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MOPS, 1.25 M magnesium sulfate	Resolution 8.76 Å R-free 0.317

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	9y74
Deposition date deposition_date	2025-09-09
Structure title title	[22L-7B C\|A] 22 bp L-DNA tensegrity triangle that propagates via blunt-end stacking with C stacking on A at the interface
Keywords keywords	dna, tensegrity triangle, stacking, blunt; DNA
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	21.64 Å
Radius of gyration Rg (electron density) rg_electron	21.92 Å
Forward intensity I(0) i0	11204200.00
Molecular weight molecular_weight	12926.0 kDa
Excluded volume excluded_volume	10117 Å³
Envelope volume envelope_volume	20634 Å³
Hydration-shell volume shell_volume	9756 Å³
Envelope diameter envelope_diameter	75.4 Å
Shell Rg shell_rg	24.56 Å
Envelope Rg envelope_rg	22.03 Å
Shape Rg shape_rg	21.87 Å
Total Rg total_rg	22.22 Å
Total atoms total_atoms	896
Residues n_residues	—
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	76.2 Å
Rg (real space) rg_real	22.14 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	1.1200e+07
I(0) uncertainty (real space) i0_real_error	1.9050e+05
Rg (reciprocal space) rg_reciprocal	22.05 Å
I(0) (reciprocal space) i0_reciprocal	11200000.0000
Solution quality estimate total_estimate	0.5190
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.8 Å
Skewness Skewness skewness	0.624
Kurtosis Kurtosis kurtosis	-0.435
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	756400.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.380; Stabil: 1.000; Sysdev: 0.207; Positv: 1.000; Valcen: 0.071; Smooth: 0.913

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D((0DC)P(0DG)P(0DA)P(0DT)P(0DG)P(0DC)P(0DC)P(0DT)P(0DG)P(0DT)P(0DA)P(0DC)P(0DG)(0DG)P(0DA)P(0DC)P(0DA)P(0DG)P(0DA)P(0DT)P(0DC)P*(0DA))-3') ;
Molecular weight formula_weight	6761.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	896

CGATGCCTGTACGGACAGATCA

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(P(0DC)P(0DC)P(0DG)P(0DT)P(0DA)P(0DC)P*(0DA))-3') ;
Molecular weight formula_weight	2082.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

CCGTACA

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(P(0DG)P(0DG)P(0DC)P(0DA)P(0DT)P(0DC)P*(0DG))-3') ;
Molecular weight formula_weight	2138.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GGCATCG

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D((0DT)P(0DG)P(0DA)P(0DT)P(0DC)P(0DT)P(0DG)P(0DT))-3') ;
Molecular weight formula_weight	2432.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TGATCTGT

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8. Citations (1)

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Unit-cell length a length_a	130.403 Å
Unit-cell length b length_b	130.403 Å
Unit-cell length c length_c	61.962 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	6

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	hexagonal

Resolution resolution	8.760 Å
Low-resolution limit resolution_low	56.470 Å
R factor r_factor	0.2383
R_work r_work	0.2366
R_free r_free	0.3171

fit	/app/data/saxs_computation/y7/9y74/9y74.fit
pddf	/app/data/pr_computation/y7/9y74/9y74.pr.out
profile	/app/data/saxs_computation/y7/9y74/9y74.dat

[22L-7B C|A] 22 bp L-DNA tensegrity triangle that propagates via blunt-end stacking with C stacking on A at the interface

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)