SAXSdb — 1m07

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

Ribonuclease

OrganismNot specified

UniProt P11916

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 1	5'-D(APCPGPA)-3' × 1 water × 2	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 1	5'-D(APCPGPA)-3' × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNASO_RANCA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–111； UniProt 1–111 Author chain B； PDBConstruct 1–111； UniProt 1–111

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	1m07
Deposition date deposition_date	2002-06-12
Structure title title	RESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTOXIC RIBONUCLEASE FROM BULLFROG (RANA CATESBEIANA)
Keywords keywords	RC-RNase-d(ACGA), ribonuclease, bullfrog, cytotoxicity, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
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.

1m07__assembly_1__model_1

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

Download this curve (.dat)

1m07__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1m07__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.80 Å
Rg (electron density)	13.81 Å
Total Rg	14.94 Å
Atom count	948
Residues	114
Excluded volume	16606 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1m07__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1m07__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	5'-D(APCPGPA)-3'
Molecular weight formula_weight	1199.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	2251

ACGA

Entity 2 Entity 2 polymer

Description description	Ribonuclease
Molecular weight formula_weight	12459.3 kDa
EC 编号 ec_number	3.1.27.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

QNWATFQQKHIINTPIINCNTIMDNNIYIVGGQCKRVNTFIISSATTVKAICTGVINMNVLSTTRFQLNTCTRTSITPRPCPYSSRTETNYICVKCENQYPVHFAGIGRCP

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	323

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1m07a_
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	d1m07b_
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	1m07A00
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	1m07B00
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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7. Citations (6)

;Residues involved in the catalysis, base specificity, and cytotoxicity of ribonuclease from Rana catesbeiana based upon mutagenesis and X-ray crystallography ;

J.Biol.Chem. (2003)

PMID: 12499382 · DOI: 10.1074/jbc.M206701200 PRIMARY

PURIFICATION AND CLONING OF CYTOTOXIC RIBONUCLEASE FROM RANA CATESBEIANA (BULLFROG)

Nucleic Acids Res. (2000)

DOI: 10.1093/nar/28.21.4097

THE SOLUTION STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYTE OF RANA CATESBEIANA (BULLFROG)

J.Mol.Biol. (1998)

DOI: 10.1006/jmbi.1998.2082

;THE RANA CATESBEIANA RCR GENE ENCODING A CYTOTOXIC RIBONUCLEASE : TISSUE DISTRIBUTION, CLONING, PURIFICATION, CYTOTOXICITY, AND ACTIVE RESIDUES FOR RNASE ACTIVITY ;

J.Biol.Chem. (1998)

DOI: 10.1074/jbc.273.11.6395

;THE SECONDARY STRUCTURE OF A PYRIMIDINE-GUANINE SEQUENCE-SPECIFIC RIBONUCLEASE POSSESSING CYTOTOXIC ACTIVITY FROM THE OOCYTE OF RANA CATESBEIANA ;

J.BIOMOL.NMR (1996)

THE CRYSTAL STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYTE OF RANA CATESBEIANA

To be Published

Unit-cell length a length_a	28.629 Å
Unit-cell length b length_b	53.566 Å
Unit-cell length c length_c	72.203 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.31 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	19.680 Å
R factor r_factor	0.2270
R_work r_work	0.1890
R_free r_free	0.2280

RESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTOXIC RIBONUCLEASE FROM BULLFROG (RANA CATESBEIANA)

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

Ribonuclease

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

1m07__assembly_1__model_1

1m07__assembly_1__model_1 | I(q)

1m07__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (6)

RESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTOXIC RIBONUCLEASE FROM BULLFROG (RANA CATESBEIANA)

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

Ribonuclease

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

1m07__assembly_1__model_1

1m07__assembly_1__model_1 | I(q)

1m07__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (6)