SAXSdb — 1di2

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

DOUBLE STRANDED RNA BINDING PROTEIN A

Xenopus laevis

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 × 2 RNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 112–180 Chain B； UniProt 112–180	Fragment：SECOND DSRNA BINDING DOMAIN Mutation：N112M	;RNA (5'-R(GPGPCPGPCPGPCPGPCPC)-3') ; × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；298 K；PEG 4000, ETHYLENE GLYCOL, KCL, NACL, MES, DTT, BETA-MERCAPTOETHANOL, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.90 Å R-free 0.258

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	TRBP_XENLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–69； UniProt 112–180 Author chain B； PDBConstruct 1–69； UniProt 112–180

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	1di2
Deposition date deposition_date	1999-11-28
Structure title title	CRYSTAL STRUCTURE OF A DSRNA-BINDING DOMAIN COMPLEXED WITH DSRNA: MOLECULAR BASIS OF DOUBLE-STRANDED RNA-PROTEIN INTERACTIONS
Keywords keywords	PROTEIN-RNA COMPLEX, DOUBLE STRANDED RNA, PROTEIN-RNA INTERACTIONS, RNA-BINING PROTEIN, RNA BINDING PROTEIN-RNA COMPLEX; RNA BINDING PROTEIN/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	24.15 Å
Radius of gyration Rg (electron density) rg_electron	24.00 Å
Forward intensity I(0) i0	22131200.00
Molecular weight molecular_weight	27138.0 kDa
Excluded volume excluded_volume	30199 Å³
Envelope volume envelope_volume	45024 Å³
Hydration-shell volume shell_volume	17492 Å³
Envelope diameter envelope_diameter	89.2 Å
Shell Rg shell_rg	27.88 Å
Envelope Rg envelope_rg	24.68 Å
Shape Rg shape_rg	23.95 Å
Total Rg total_rg	24.51 Å
Total atoms total_atoms	1856
Residues n_residues	169
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	87.7 Å
Rg (real space) rg_real	24.49 Å
Rg uncertainty (real space) rg_real_error	0.89 Å
I(0) (real space) i0_real	2.2130e+07
I(0) uncertainty (real space) i0_real_error	2.9670e+05
Rg (reciprocal space) rg_reciprocal	24.41 Å
I(0) (reciprocal space) i0_reciprocal	22130000.0000
Solution quality estimate total_estimate	0.8114
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.678
Kurtosis Kurtosis kurtosis	0.211
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	907200.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.675; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.656; Smooth: 0.864

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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	;RNA (5'-R(GPGPCPGPCPGPCPGPCPC)-3') ;
Molecular weight formula_weight	3207.0 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,D,E,G
Atom count atom_count	2243

GGCGCGCGCC

Entity 2 Entity 2 polymer

Description description	DOUBLE STRANDED RNA BINDING PROTEIN A
Molecular weight formula_weight	7689.9 kDa
Mutation mutation	N112M
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MPVGSLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVETFVETGSGTSKQVAKRVAAEKLLTKFKT

来源 Source

来源生物 organism	Xenopus laevis
通用名 common_name	African clawed frog
NCBI Class编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	359

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1di2a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.50 — dsRBD-like
Superfamily Superfamily superfamily	d.50.1 — dsRNA-binding domain-like
Family Family family	d.50.1.1 — Double-stranded RNA-binding domain (dsRBD)

Domain ID domain_id	d1di2b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.50 — dsRBD-like
Superfamily Superfamily superfamily	d.50.1 — dsRNA-binding domain-like
Family Family family	d.50.1.1 — Double-stranded RNA-binding domain (dsRBD)

CATH v4.4 (2 domains)

Domain ID domain_id	1di2A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1di2B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	110.400 Å
Unit-cell length b length_b	58.500 Å
Unit-cell length c length_c	58.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2310
R_work r_work	0.2280
R_free r_free	0.2580

fit	/app/data/saxs_computation/di/1di2/1di2.fit
pddf	/app/data/pr_computation/di/1di2/1di2.pr.out
profile	/app/data/saxs_computation/di/1di2/1di2.dat

CRYSTAL STRUCTURE OF A DSRNA-BINDING DOMAIN COMPLEXED WITH DSRNA: MOLECULAR BASIS OF DOUBLE-STRANDED RNA-PROTEIN INTERACTIONS

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

DOUBLE STRANDED RNA BINDING PROTEIN A

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)