SAXSdb — 1ddl

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

DESMODIUM YELLOW MOTTLE VIRUS

OrganismNot specified

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–RNA Homooligomer Protein × 180 RNA 120 PDB declaration: 300-MERIC（300） Consistent with all polymer counts	Chain A； UniProt 1–188 Chain B； UniProt 1–188 Chain C； UniProt 1–188	Fragment：VIRAL COAT PROTEIN	;RNA (5'-R(PUPUPUPUPUPUPU)-3') ; × 60 ;RNA (5'-R(PUP*U)-3') ; × 60	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP；pH 4.8；295 K；2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, POTASSIUM PHOSPHATE BUFFER, pH 4.8, VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.159
2	Protein–RNA Homooligomer Protein × 3 RNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 1–188 Chain B； UniProt 1–188 Chain C； UniProt 1–188	Fragment：VIRAL COAT PROTEIN	;RNA (5'-R(PUPUPUPUPUPUPU)-3') ; × 1 ;RNA (5'-R(PUP*U)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP；pH 4.8；295 K；2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, POTASSIUM PHOSPHATE BUFFER, pH 4.8, VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.159
3	Protein–RNA Homooligomer Protein × 15 RNA 10 PDB declaration: 25-meric（25） Consistent with all polymer counts	Chain A； UniProt 1–188 Chain B； UniProt 1–188 Chain C； UniProt 1–188	Fragment：VIRAL COAT PROTEIN	;RNA (5'-R(PUPUPUPUPUPUPU)-3') ; × 5 ;RNA (5'-R(PUP*U)-3') ; × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP；pH 4.8；295 K；2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, POTASSIUM PHOSPHATE BUFFER, pH 4.8, VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.159
4	Protein–RNA Homooligomer Protein × 18 RNA 12 PDB declaration: 30-meric（30） Consistent with all polymer counts	Chain A； UniProt 1–188 Chain B； UniProt 1–188 Chain C； UniProt 1–188	Fragment：VIRAL COAT PROTEIN	;RNA (5'-R(PUPUPUPUPUPUPU)-3') ; × 6 ;RNA (5'-R(PUP*U)-3') ; × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP；pH 4.8；295 K；2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, POTASSIUM PHOSPHATE BUFFER, pH 4.8, VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.159
5	Protein–RNA Homooligomer Protein × 3 RNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 1–188 Chain B； UniProt 1–188 Chain C； UniProt 1–188	Fragment：VIRAL COAT PROTEIN	;RNA (5'-R(PUPUPUPUPUPUPU)-3') ; × 1 ;RNA (5'-R(PUP*U)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP；pH 4.8；295 K；2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, POTASSIUM PHOSPHATE BUFFER, pH 4.8, VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.159
6	Protein–RNA Homooligomer Protein × 15 RNA 10 PDB declaration: 25-meric（25） Consistent with all polymer counts	Chain A； UniProt 1–188 Chain B； UniProt 1–188 Chain C； UniProt 1–188	Fragment：VIRAL COAT PROTEIN	;RNA (5'-R(PUPUPUPUPUPUPU)-3') ; × 5 ;RNA (5'-R(PUP*U)-3') ; × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP；pH 4.8；295 K；2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, POTASSIUM PHOSPHATE BUFFER, pH 4.8, VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.159

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	O89511_9VIRU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–188； UniProt 1–188 Author chain B； PDBConstruct 1–188； UniProt 1–188 Author chain C； PDBConstruct 1–188； UniProt 1–188

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	1ddl
Deposition date deposition_date	1999-11-10
Structure title title	DESMODIUM YELLOW MOTTLE TYMOVIRUS
Keywords keywords	PLANT VIRUS, DYMV, CAPSID PROTEIN, COAT PROTEIN, TYMOVIRUSES, WATER STRUCTURE, RNA, Icosahedral virus, Virus-RNA COMPLEX; Virus/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	30.47 Å
Radius of gyration Rg (electron density) rg_electron	29.78 Å
Forward intensity I(0) i0	59846400.00
Molecular weight molecular_weight	61325.0 kDa
Excluded volume excluded_volume	76895 Å³
Envelope volume envelope_volume	100130 Å³
Hydration-shell volume shell_volume	28926 Å³
Envelope diameter envelope_diameter	100.2 Å
Shell Rg shell_rg	35.51 Å
Envelope Rg envelope_rg	29.96 Å
Shape Rg shape_rg	29.73 Å
Total Rg total_rg	30.47 Å
Total atoms total_atoms	4307
Residues n_residues	560
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	97.4 Å
Rg (real space) rg_real	30.47 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	5.9850e+07
I(0) uncertainty (real space) i0_real_error	9.7330e+05
Rg (reciprocal space) rg_reciprocal	30.48 Å
I(0) (reciprocal space) i0_reciprocal	59850000.0000
Solution quality estimate total_estimate	0.9027
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.1 Å
Skewness Skewness skewness	0.214
Kurtosis Kurtosis kurtosis	-0.718
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8467000.0000
Real-space data points n_real_points	53
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: 0.939; Smooth: 0.947

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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	;RNA (5'-R(PUPUPUPUPUPUP*U)-3') ;
Molecular weight formula_weight	2098.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	4670

UUUUUUU

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(PUPU)-3') ;
Molecular weight formula_weight	567.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E

UU

Entity 3 Entity 3 polymer

Description description	DESMODIUM YELLOW MOTTLE VIRUS
Molecular weight formula_weight	20011.7 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C

MEQDKILAHQASLNTKPSLLPPPVGNPPPVISYPFQITLASLGTEDAADSVSIASNSVLATYTALYRHAQLKHLKATIHPTYMAPKYPTSVALVWVPANSTATSTQVLDTYGGLHFCIGGSVNSVKPIDVEANLTNLNPIIKASTTFTDTPKLLYYSKAQATAPTSPTCYLTIQGQIELSSPLLQASS

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	285

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1ddla_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.6 — Tymoviridae-like VP

Domain ID domain_id	d1ddlb_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.6 — Tymoviridae-like VP

Domain ID domain_id	d1ddlc_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.6 — Tymoviridae-like VP

CATH v4.4 (3 domains)

Domain ID domain_id	1ddlA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1ddlB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1ddlC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	348.546 Å
Unit-cell length b length_b	348.546 Å
Unit-cell length c length_c	348.546 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	360

Space group space_group	P 42 3 2
Space-group number int_tables_number	208
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1520
R_work r_work	0.1510
R_free r_free	0.1590

fit	/app/data/saxs_computation/dd/1ddl/1ddl.fit
pddf	/app/data/pr_computation/dd/1ddl/1ddl.pr.out
profile	/app/data/saxs_computation/dd/1ddl/1ddl.dat

DESMODIUM YELLOW MOTTLE TYMOVIRUS

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

DESMODIUM YELLOW MOTTLE VIRUS

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 (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 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)