1ry3

NMR Solution Structure of the Precursor for Carnobacteriocin B2, an Antimicrobial Peptide from Carnobacterium piscicola

Method: SOLUTION NMR D_max: 101.5 Å Quality: REASONABLE

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

Bacteriocin carnobacteriocin B2

Carnobacterium maltaromaticum

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 1–64	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 2；308 K；Pressure ambient NMR sample composition：1 mM precarnobacteriocin B2 U-15N \| 70% TFE-d3, 30% H2O NMR sample composition：1 mM precarnobacteriocin B2 U-15N,U-13C \| 70% TFE-d3, 30% 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 1RY3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CW5 SOLUTION STRUCTURE OF CARNOBACTERIOCIN B2 Deposited 1999-08-25	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–66（48 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 2.8；298 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR sample composition 5.0 MG CARNOBACTERIOCIN B2 IS DISOLVED IN 700 UL OF TFE-D3/H2O, 90%:10% V/V, PH 2.8.	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	CBB2_CARPI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–63； UniProt 1–64

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	1ry3
Deposition date deposition_date	2003-12-19
Structure title title	NMR Solution Structure of the Precursor for Carnobacteriocin B2, an Antimicrobial Peptide from Carnobacterium piscicola
Keywords keywords	amphipathic helix, ANTIBIOTIC; ANTIBIOTIC
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	24.05 Å
Radius of gyration Rg (electron density) rg_electron	24.03 Å
Forward intensity I(0) i0	310872000.00
Molecular weight molecular_weight	134890.0 kDa
Excluded volume excluded_volume	165180 Å³
Envelope volume envelope_volume	122660 Å³
Hydration-shell volume shell_volume	35088 Å³
Envelope diameter envelope_diameter	109.0 Å
Shell Rg shell_rg	35.79 Å
Envelope Rg envelope_rg	30.58 Å
Shape Rg shape_rg	23.86 Å
Total Rg total_rg	25.18 Å
Total atoms total_atoms	18660
Residues n_residues	1280
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	101.5 Å
Rg (real space) rg_real	24.36 Å
Rg uncertainty (real space) rg_real_error	1.55 Å
I(0) (real space) i0_real	3.1090e+08
I(0) uncertainty (real space) i0_real_error	5.7400e+06
Rg (reciprocal space) rg_reciprocal	24.29 Å
I(0) (reciprocal space) i0_reciprocal	310900000.0000
Solution quality estimate total_estimate	0.7235
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.0 Å
Skewness Skewness skewness	0.519
Kurtosis Kurtosis kurtosis	0.133
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	147300.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.377; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.311; Smooth: 0.959

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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_id	d1ry3a_
Class class	j — Peptides
Fold Fold fold	j.106 — Leucocin-like bacteriocin
Superfamily Superfamily superfamily	j.106.1 — Leucocin-like bacteriocin
Family Family family	j.106.1.1 — Leucocin-like bacteriocin

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	Bacteriocin carnobacteriocin B2
Molecular weight formula_weight	6748.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	18660

来源生物 organism	Carnobacterium maltaromaticum
NCBI Class编号 ncbi_taxonomy_id	2751
宿主生物 host_organism	Escherichia coli BL21(DE3)

NMR Solution Structure of the Precursor for Carnobacteriocin B2, an Antimicrobial Peptide from Carnobacterium piscicola

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

Bacteriocin carnobacteriocin B2

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/ry/1ry3/1ry3.fit
pddf	/app/data/pr_computation/ry/1ry3/1ry3.pr.out
profile	/app/data/saxs_computation/ry/1ry3/1ry3.dat