1bol

THE CRYSTAL STRUCTURE OF RIBONUCLEASE RH FROM RHIZOPUS NIVEUS AT 2.0 A RESOLUTION

Method: X-RAY DIFFRACTION D_max: 64.2 Å Quality: GOOD

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

PROTEIN (RIBONUCLEASE RH)

OrganismNot specified

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 17–238	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.7；pH 6.7	Resolution 2.00 Å

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	RNRH_RHINI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–222； UniProt 17–238

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bol
Deposition date deposition_date	1998-08-05
Structure title title	THE CRYSTAL STRUCTURE OF RIBONUCLEASE RH FROM RHIZOPUS NIVEUS AT 2.0 A RESOLUTION
Keywords keywords	RIBONUCLEASES, 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	18.63 Å
Radius of gyration Rg (electron density) rg_electron	17.35 Å
Forward intensity I(0) i0	11696800.00
Molecular weight molecular_weight	24069.0 kDa
Excluded volume excluded_volume	29350 Å³
Envelope volume envelope_volume	33811 Å³
Hydration-shell volume shell_volume	16528 Å³
Envelope diameter envelope_diameter	61.1 Å
Shell Rg shell_rg	23.21 Å
Envelope Rg envelope_rg	17.58 Å
Shape Rg shape_rg	17.31 Å
Total Rg total_rg	18.31 Å
Total atoms total_atoms	1688
Residues n_residues	222
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	64.2 Å
Rg (real space) rg_real	18.56 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.1700e+07
I(0) uncertainty (real space) i0_real_error	1.4800e+05
Rg (reciprocal space) rg_reciprocal	18.58 Å
I(0) (reciprocal space) i0_reciprocal	11700000.0000
Solution quality estimate total_estimate	0.7955
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.0 Å
Skewness Skewness skewness	0.227
Kurtosis Kurtosis kurtosis	-0.411
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2229000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.784; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bola_
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	1bolA00
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 (1)

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Unit-cell length a length_a	67.700 Å
Unit-cell length b length_b	72.500 Å
Unit-cell length c length_c	44.300 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	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1850
R_work r_work	0.1850
R_free r_free	—

Description description	PROTEIN (RIBONUCLEASE RH)
Molecular weight formula_weight	24096.2 kDa
EC 编号 ec_number	3.1.27.1
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1688

THE CRYSTAL STRUCTURE OF RIBONUCLEASE RH FROM RHIZOPUS NIVEUS AT 2.0 A RESOLUTION

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

PROTEIN (RIBONUCLEASE RH)

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/bo/1bol/1bol.fit
pddf	/app/data/pr_computation/bo/1bol/1bol.pr.out
profile	/app/data/saxs_computation/bo/1bol/1bol.dat