SAXSdb — 1dix

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

EXTRACELLULAR RIBONUCLEASE LE

Solanum lycopersicum

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 27–230	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；PEG1540, CITRATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.278

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	RNLE_LYCES
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–208； UniProt 27–230

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	1dix
Deposition date deposition_date	1999-11-30
Structure title title	CRYSTAL STRUCTURE OF RNASE LE
Keywords keywords	ALPHA PLUS BETA, HYDROLASE; HYDROLASE
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	18.07 Å
Radius of gyration Rg (electron density) rg_electron	16.65 Å
Forward intensity I(0) i0	10154200.00
Molecular weight molecular_weight	22886.0 kDa
Excluded volume excluded_volume	28197 Å³
Envelope volume envelope_volume	31959 Å³
Hydration-shell volume shell_volume	16138 Å³
Envelope diameter envelope_diameter	55.7 Å
Shell Rg shell_rg	22.63 Å
Envelope Rg envelope_rg	16.79 Å
Shape Rg shape_rg	16.61 Å
Total Rg total_rg	17.69 Å
Total atoms total_atoms	1612
Residues n_residues	208
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	56.0 Å
Rg (real space) rg_real	17.94 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	1.0150e+07
I(0) uncertainty (real space) i0_real_error	1.1250e+05
Rg (reciprocal space) rg_reciprocal	17.96 Å
I(0) (reciprocal space) i0_reciprocal	10150000.0000
Solution quality estimate total_estimate	0.9051
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.0 Å
Skewness Skewness skewness	0.112
Kurtosis Kurtosis kurtosis	-0.510
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1865000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 1.000

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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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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1dixa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.124 — Ribonuclease Rh-like
Superfamily Superfamily superfamily	d.124.1 — Ribonuclease Rh-like
Family Family family	d.124.1.1 — Ribonuclease Rh-like

CATH v4.4 (1 domains)

Domain ID domain_id	1dixA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	730 — Ribonuclease Rh; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease T2-like

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8. Citations (2)

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Unit-cell length a length_a	74.020 Å
Unit-cell length b length_b	78.790 Å
Unit-cell length c length_c	32.930 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.2190
R_free r_free	0.2780

Description description	EXTRACELLULAR RIBONUCLEASE LE
Molecular weight formula_weight	22912.2 kDa
EC 编号 ec_number	3.1.27.1
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1748

CRYSTAL STRUCTURE OF RNASE LE

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

EXTRACELLULAR RIBONUCLEASE LE

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Solanum lycopersicum
NCBI Class编号 ncbi_taxonomy_id	4081
宿主生物 host_organism	Saccharomyces cerevisiae

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	136

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