SAXSdb — 3fd7

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

Protein P-30

Rana pipiens

UniProt P22069

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 5 GLYCEROL × 2 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 2 GLYCEROL × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 7 GLYCEROL × 3 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNP30_RANPI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–104； UniProt 1–104 Author chain B； PDBConstruct 1–104； UniProt 1–104

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	3fd7
Deposition date deposition_date	2008-11-25
Structure title title	Crystal structure of Onconase C87A/C104A-ONC
Keywords keywords	Onconase, C-terminal disulfide bond, Endonuclease, Hydrolase, Nuclease, Pyrrolidone carboxylic acid; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3fd7__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3fd7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fd7__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	15.12 Å
Rg (electron density)	13.83 Å
Total Rg	15.16 Å
Atom count	859
Residues	102
Excluded volume	15205 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fd7__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fd7__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3fd7__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Protein P-30
Molecular weight formula_weight	11781.5 kDa
EC 编号 ec_number	3.1.27.-
Mutation mutation	C87A, C104A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2115

QDWLTFQKKHITNTRDVDCDNIMSTNLFHCKDKNTFIYSRPEPVKAICKGIIASKNVLTTSEFYLSDCNVTSRPCKYKLKKSTNKFAVTCENQAPVHFVGVGSA

Source Source

Source organism organism	Rana pipiens
Common name common_name	Northern leopard frog
NCBI taxonomy ID ncbi_taxonomy_id	8404
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	355

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3fd7a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.5 — RNase A-like
Superfamily Superfamily superfamily	d.5.1 — RNase A-like
Family Family family	d.5.1.1 — Ribonuclease A-like

Domain ID domain_id	d3fd7b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.5 — RNase A-like
Superfamily Superfamily superfamily	d.5.1 — RNase A-like
Family Family family	d.5.1.1 — Ribonuclease A-like

CATH v4.4 (2 domains)

Domain ID domain_id	3fd7A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	130 — P-30 Protein
Homologous superfamily homologous superfamily	10 — Ribonuclease A-like domain

Domain ID domain_id	3fd7B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	130 — P-30 Protein
Homologous superfamily homologous superfamily	10 — Ribonuclease A-like domain

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Unit-cell length a length_a	45.460 Å
Unit-cell length b length_b	51.190 Å
Unit-cell length c length_c	87.690 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	8

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

Resolution resolution	1.531 Å
Low-resolution limit resolution_low	26.864 Å
R factor r_factor	0.1400
R_work r_work	0.1380
R_free r_free	0.1880

Crystal structure of Onconase C87A/C104A-ONC

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

Protein P-30

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3fd7__assembly_1__model_1

3fd7__assembly_1__model_1 | I(q)

3fd7__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Onconase C87A/C104A-ONC

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

Protein P-30

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3fd7__assembly_1__model_1

3fd7__assembly_1__model_1 | I(q)

3fd7__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)