4huo

Structure of Ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)-L-phenylalanine

Method: X-RAY DIFFRACTION Dmax: 68.1 Å Quality: GOOD

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

Ricin

Ricinus communis

UniProt P02879

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 X; UniProt 36–302 Not recorded RS8 N-[(2-amino-4-oxo-1,4-dihydropteridin-7-yl)carbonyl]glycyl-L-phenylalanine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;277 K;1.3 M Ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 1.52 Å R-free 0.230
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain X; UniProt 36–302 Not recorded RS8 N-[(2-amino-4-oxo-1,4-dihydropteridin-7-yl)carbonyl]glycyl-L-phenylalanine × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;277 K;1.3 M Ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 1.52 Å R-free 0.230

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.

100 other PDB entries and 125 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RICI_RICCO
Isoform
PDB entities 1
Chains and sequence ranges Author chain X; PDBConstruct 1–267; UniProt 36–302

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

SAXS profile for 4huo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4huo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4huo
Deposition date deposition_date2012-11-02
Structure title titleStructure of Ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)-L-phenylalanine
Keywords keywords;RICIN, PROTEIN-LIGAND COMPLEX, PTERIN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, TOXIN, HYDROLASE, RIBOSOME-INACTIVATING PROTEIN, N-GLYCOSIDASE ;; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.61
Radius of gyration Rg (electron density) rg_electron18.34
Forward intensity I(0) i015900900.00
Molecular weight molecular_weight29818.0 kDa
Excluded volume excluded_volume37214 ų
Envelope volume envelope_volume43254 ų
Hydration-shell volume shell_volume19465 ų
Envelope diameter envelope_diameter71.8
Shell Rg shell_rg25.05
Envelope Rg envelope_rg19.03
Shape Rg shape_rg18.35
Total Rg total_rg19.27
Total atoms total_atoms2108
Residues n_residues263
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax68.1
Rg (real space) rg_real19.52
Rg uncertainty (real space) rg_real_error0.49
I(0) (real space) i0_real1.5900e+07
I(0) uncertainty (real space) i0_real_error1.9760e+05
Rg (reciprocal space) rg_reciprocal19.53
I(0) (reciprocal space) i0_reciprocal15900000.0000
Solution quality estimate total_estimate0.7751
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.9
Skewness Skewness skewness0.274
Kurtosis Kurtosis kurtosis-0.155
Angular range angular_range— – 0.4050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4312000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.695; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4huox_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamilyd.165.1 — Ribosome inactivating proteins (RIP)
Family Family familyd.165.1.1 — Plant cytotoxins

CATH v4.4 (2 domains)

Domain ID domain_id4huoX01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily10 — Ricin (A subunit), domain 1
Domain ID domain_id4huoX02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily10 — Ricin (A Subunit), domain 2

8. Citations (1)

9. Files and Curves (10)