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1nbj

High-resolution solution structure of cycloviolacin O1

Method: SOLUTION NMR Dmax: 26.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

cycloviolacin O1

OrganismNot specified

UniProt P82230

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 4–30 Chain A； UniProt 1–3 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 5.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition：1.3mM in total volume of 0.5ml | 90% H2O/10% D2O NMR sample composition：1.3mM in total volume of 0.5ml | 100% D2O Resolution not provided

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 1NBJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DF6 1H NMR SOLUTION STRUCTURE OF CYCLOVIOLACIN O1 Deposited 1999-11-17 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–30（24 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3.6；298 K；Pressure AMBIENT
NMR sample composition 1.6MM CYCLOVIOLACIN O1 1H
NMR sample composition 1.6MM CYCLOVIOLACIN O1 1H
Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYO1_VIOOD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–27； UniProt 4–30 Author chain A； PDBConstruct 28–30； UniProt 1–3

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 1nbj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1nbj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1nbj
Deposition date deposition_date2002-12-02
Structure title titleHigh-resolution solution structure of cycloviolacin O1
Keywords keywordscyclotide, cyclic backbone, cystine knot, CCK, PLANT PROTEIN; PLANT PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier6.99 Å
Radius of gyration Rg (electron density) rg_electron8.20 Å
Forward intensity I(0) i063417300.00
Molecular weight molecular_weight62474.0 kDa
Excluded volume excluded_volume76372 ų
Envelope volume envelope_volume5262 ų
Hydration-shell volume shell_volume5402 ų
Envelope diameter envelope_diameter30.9 Å
Shell Rg shell_rg13.76 Å
Envelope Rg envelope_rg9.55 Å
Shape Rg shape_rg8.26 Å
Total Rg total_rg8.16 Å
Total atoms total_atoms8320
Residues n_residues600
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax26.2 Å
Rg (real space) rg_real6.97 Å
Rg uncertainty (real space) rg_real_error0.34 Å
I(0) (real space) i0_real6.3420e+07
I(0) uncertainty (real space) i0_real_error6.4310e+05
Rg (reciprocal space) rg_reciprocal6.97 Å
I(0) (reciprocal space) i0_reciprocal63420000.0000
Solution quality estimate total_estimate0.7443
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary9.3 Å
Skewness Skewness skewness0.190
Kurtosis Kurtosis kurtosis-0.314
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4586.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.588; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.911; 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) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1nbja_
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.3 — Cyclotides
Family Family familyg.3.3.2 — Cycloviolacin
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8. Citations (1)

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9. Files and Curves (10)