SAXSdb — 1jbr

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

Restrictocin

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–RNA Monomer Protein × 1 RNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 28–176	Not recorded	5'-R(GPCPGPCPUPCPCPUPCPAPGPUPAPCPGPAPGP(A23))-3' × 1 5'-R(GPGPAPAPCPCPGPGPAPGPCPGP*C)-3' × 1 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG5000, K-MES, KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.15 Å R-free 0.290
2	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 28–176	Not recorded	31-mer SRD RNA analog × 1 K POTASSIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG5000, K-MES, KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.15 Å R-free 0.290

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 1JBR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AQZ CRYSTAL STRUCTURE OF A HIGHLY SPECIFIC ASPERGILLUS RIBOTOXIN, RESTRICTOCIN Deposited 1997-08-04	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 28–176（149 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion and microdialysis；pH 6.8；A COMBINATION OF VAPOR DIFFUSION AND MICRODIALYSIS TECHNIQUES WERE USED TO CRYSTALLIZE RESTRICTOCIN. THE FINAL MOTHER LIQUOR CONSISTS OF 60% ETHANOL, 10MM SODIUM PHOSPHATE, PH6.8. THE PROTEIN CONCENTRATION IS 10MG/ML., vapor diffusion and microdialysis	Resolution 1.70 Å R-free 0.177
1AQZ CRYSTAL STRUCTURE OF A HIGHLY SPECIFIC ASPERGILLUS RIBOTOXIN, RESTRICTOCIN Deposited 1997-08-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–176（149 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion and microdialysis；pH 6.8；A COMBINATION OF VAPOR DIFFUSION AND MICRODIALYSIS TECHNIQUES WERE USED TO CRYSTALLIZE RESTRICTOCIN. THE FINAL MOTHER LIQUOR CONSISTS OF 60% ETHANOL, 10MM SODIUM PHOSPHATE, PH6.8. THE PROTEIN CONCENTRATION IS 10MG/ML., vapor diffusion and microdialysis	Resolution 1.70 Å R-free 0.177
1JBT CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG Deposited 2001-06-06	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 28–176（149 aa）	Not recorded	K POTASSIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG5000, K.MES, KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.282
1JBT CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN COMPLEXED WITH A 29-MER SARCIN/RICIN DOMAIN RNA ANALOG Deposited 2001-06-06	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 28–176（149 aa）	Not recorded	K POTASSIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；PEG5000, K.MES, KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.70 Å R-free 0.282

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RNMG_ASPRE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 28–176 Author chain B； PDBConstruct 1–149； UniProt 28–176

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	1jbr
Deposition date deposition_date	2001-06-06
Structure title title	Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor
Keywords keywords	;protein-RNA interaction, specific recognition, restrictocin, ribosomal RNA, sarcin/ricin domain, base flipping, HYDROLASE-RNA COMPLEX ;; HYDROLASE/RNA
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	40.88 Å
Radius of gyration Rg (electron density) rg_electron	44.63 Å
Forward intensity I(0) i0	73576400.00
Molecular weight molecular_weight	54004.0 kDa
Excluded volume excluded_volume	60773 Å³
Envelope volume envelope_volume	96923 Å³
Hydration-shell volume shell_volume	21282 Å³
Envelope diameter envelope_diameter	135.1 Å
Shell Rg shell_rg	40.57 Å
Envelope Rg envelope_rg	42.93 Å
Shape Rg shape_rg	44.82 Å
Total Rg total_rg	44.01 Å
Total atoms total_atoms	3715
Residues n_residues	359
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	133.1 Å
Rg (real space) rg_real	41.55 Å
Rg uncertainty (real space) rg_real_error	1.61 Å
I(0) (real space) i0_real	7.3580e+07
I(0) uncertainty (real space) i0_real_error	1.3650e+06
Rg (reciprocal space) rg_reciprocal	40.88 Å
I(0) (reciprocal space) i0_reciprocal	73520000.0000
Solution quality estimate total_estimate	0.5976
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.9 Å
Skewness Skewness skewness	0.491
Kurtosis Kurtosis kurtosis	-0.898
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1521000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.237; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.036; Smooth: 0.020

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	5'-R(GPCPGPCPUPCPCPUPCPAPGPUPAPCPGPAPGP(A23))-3'
Molecular weight formula_weight	5809.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	3883

GCGCUCCUCAGUACGAGA

Entity 2 Entity 2 polymer

Description description	5'-R(GPGPAPAPCPCPGPGPAPGPCPGP*C)-3'
Molecular weight formula_weight	4234.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	F

GGAACCGGAGCGC

Entity 3 Entity 3 polymer

Description description	31-mer SRD RNA analog
Molecular weight formula_weight	10027.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D

GCGCUCCUCAGUACGAGAGGAACCGGAGCGC

Entity 4 Entity 4 polymer

Description description	Restrictocin
Molecular weight formula_weight	16889.9 kDa
EC 编号 ec_number	3.1.27.-
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

ATWTCINQQLNPKTNKWEDKRLLYSQAKAESNSHHAPLSDGKTGSSYPHWFTNGYDGNGKLIKGRTPIKFGKADCDRPPKHSQNGMGKDDHYLLEFPTFPDGHDYKFDSKKPKEDPGPARVIYTYPNKVFCGIVAHQRGNQGDLRLCSH

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	168

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1jbra_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.1 — Microbial ribonucleases
Superfamily Superfamily superfamily	d.1.1 — Microbial ribonucleases
Family Family family	d.1.1.3 — Ribotoxin

Domain ID domain_id	d1jbrb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.1 — Microbial ribonucleases
Superfamily Superfamily superfamily	d.1.1 — Microbial ribonucleases
Family Family family	d.1.1.3 — Ribotoxin

CATH v4.4 (2 domains)

Domain ID domain_id	1jbrA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	30 — Microbial ribonucleases

Domain ID domain_id	1jbrB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	30 — Microbial ribonucleases

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8. Citations (1)

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Unit-cell length a length_a	60.400 Å
Unit-cell length b length_b	109.700 Å
Unit-cell length c length_c	40.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.80 °
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	2.150 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.2380
R_work r_work	0.2320
R_free r_free	0.2900

fit	/app/data/saxs_computation/jb/1jbr/1jbr.fit
pddf	/app/data/pr_computation/jb/1jbr/1jbr.pr.out
profile	/app/data/saxs_computation/jb/1jbr/1jbr.dat

Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor

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

Restrictocin

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)