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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 1–111	Non-standard monomer：Yes (specific site not provided by mmCIF)	5'-D(APCPGPA)-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；0.1 M potassium sodium tartrate tetrahydrate, 24 % PEG 8000, 0.05 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.228
2	Protein–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 1–111	Non-standard monomer：Yes (specific site not provided by mmCIF)	5'-D(APCPGPA)-3' × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；0.1 M potassium sodium tartrate tetrahydrate, 24 % PEG 8000, 0.05 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.228

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.

Other PDB	Difference from Current Entry 1M07	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BC4 THE SOLUTION STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYTES OF RANA CATESBEIANA (BULLFROG), NMR, 15 STRUCTURES Deposited 1998-05-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–111（110 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.5；305 K；Ionic strength (raw mmCIF value) 50mM PHOSPHATE BUFFER；Pressure 1 NMR sample composition H2O	Resolution not provided
1KM8 The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana Catesbeiana (Bullfrog) Deposited 2001-12-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–111（111 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ammonium phosphate, Tris hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.90 Å R-free 0.205
1KM9 The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana Catesbeiana (Bullfrog) Deposited 2001-12-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–111（111 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEG 4000, ammonium phosphate, NaOAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.96 Å R-free 0.216

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.71 Å
Radius of gyration Rg (electron density) rg_electron	20.55 Å
Forward intensity I(0) i0	15200100.00
Molecular weight molecular_weight	27279.0 kDa
Excluded volume excluded_volume	33212 Å³
Envelope volume envelope_volume	40147 Å³
Hydration-shell volume shell_volume	17223 Å³
Envelope diameter envelope_diameter	69.6 Å
Shell Rg shell_rg	25.62 Å
Envelope Rg envelope_rg	20.53 Å
Shape Rg shape_rg	20.55 Å
Total Rg total_rg	21.22 Å
Total atoms total_atoms	1896
Residues n_residues	228
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	68.2 Å
Rg (real space) rg_real	20.77 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.5200e+07
I(0) uncertainty (real space) i0_real_error	1.8170e+05
Rg (reciprocal space) rg_reciprocal	20.76 Å
I(0) (reciprocal space) i0_reciprocal	15200000.0000
Solution quality estimate total_estimate	0.8815
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.7 Å
Skewness Skewness skewness	0.413
Kurtosis Kurtosis kurtosis	-0.426
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4819000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.969

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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	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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7. 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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8. 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

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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

fit	/app/data/saxs_computation/m0/1m07/1m07.fit
pddf	/app/data/pr_computation/m0/1m07/1m07.pr.out
profile	/app/data/saxs_computation/m0/1m07/1m07.dat

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

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

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (6)

9. Files and Curves (10)

Files (7)

Curves (3)