SAXSdb — 2ly6

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

Defensin-like protein

Pentadiplandra brazzeana

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 2–54	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5.2；276 K；Ionic strength (raw mmCIF value) 5；Pressure ambient NMR measurement conditions：pH 5.2；276 K；Ionic strength (raw mmCIF value) 5；Pressure ambient NMR sample composition：1-2 mM [U-13C; U-15N] protein, 5 mM sodium chloride, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition：1-2 mM [U-13C; U-15N] protein, 5 mM sodium chloride, 93% H2O/7% D2O \| 93% H2O/7% 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 2LY6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BRZ SOLUTION STRUCTURE OF THE SWEET PROTEIN BRAZZEIN, NMR, 43 STRUCTURES Deposited 1998-03-12	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–54（53 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.2；295 K	Resolution not provided
2BRZ SOLUTION NMR STRUCTURE OF THE SWEET PROTEIN BRAZZEIN, MINIMIZED AVERAGE STRUCTURE Deposited 1998-04-30	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–54（53 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.2；295 K	Resolution not provided
2KGQ Refined solution structure of des-pyro Glu brazzein Deposited 2009-03-13	Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–54（53 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.2；310 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR measurement conditions pH 5.2；310 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 2 mM [U-13C; U-15N] wt-brazzein-1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-15N] wt-brazzein-2, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 1 mM [U-15N] wt-brazzein-3, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KYQ 1H, 15N, 13C chemical shifts and structure of CKR-brazzein Deposited 2010-06-07	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–54（53 aa）	Mutation：K3C, C4K, K5R	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.2；310 K；Pressure ambient NMR sample composition mM [U-99% 13C; U-99% 15N] CKR-brazzein, 17 uM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition mM [U-99% 15N] CKR-brazzein, 17 uM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LY5 Refined solution structure of recombinant brazzein Deposited 2012-09-12	Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–54（53 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.2；310 K；Ionic strength (raw mmCIF value) 5；Pressure ambient NMR measurement conditions pH 5.2；310 K；Ionic strength (raw mmCIF value) 5；Pressure ambient NMR sample composition 1-2 mM [U-13C; U-15N] protein, 5 mM sodium chloride, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 1-2 mM [U-13C; U-15N] protein, 5 mM sodium chloride, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
2N66 NMR Structure of sweeter mutant (D40K) of sweet protein Brazzein, Deposited 2015-08-13	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：D40K	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.2；310 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] D40K-1, 1.5 mM [U-100% 13C; U-100% 15N] D40K-2, 1.5 mM [U-100% 13C; U-100% 15N] D40K-3, 1.5 mM [U-100% 13C; U-100% 15N] D40K-4, 1.5 mM [U-100% 13C; U-100% 15N] D40K-5, 1.5 mM [U-100% 13C; U-100% 15N] D40K-6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N69 NMR structure of non-sweet mutant (ins18RI19) of sweet protein Brazzein Deposited 2015-08-14	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.2；310 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-1, 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-2, 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-3, 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-4, 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-5, 1.5 mM [U-100% 13C; U-100% 15N] Brz_RI-6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4HE7 Crystal Structure of Brazzein Deposited 2012-10-03	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：Q1E Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；0.9-1.0M sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.252
7W8E Sweet taste protein Brazzein - R43A Deposited 2021-12-07	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：R43A	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；1.5M NaCl, 1M Na-Citrate pH4.0	Resolution 1.34 Å R-free 0.225
7W8H Sweet taste protein Brazzein mutant - D29K Deposited 2021-12-07	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–54（54 aa）	Mutation：D29K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0-1.5M NaCl 1M Na-Acetate pH4.5	Resolution 1.50 Å R-free 0.268
7W8H Sweet taste protein Brazzein mutant - D29K Deposited 2021-12-07	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–54（54 aa）	Mutation：D29K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0-1.5M NaCl 1M Na-Acetate pH4.5	Resolution 1.50 Å R-free 0.268
7W8H Sweet taste protein Brazzein mutant - D29K Deposited 2021-12-07	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–54（54 aa）	Mutation：D29K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0-1.5M NaCl 1M Na-Acetate pH4.5	Resolution 1.50 Å R-free 0.268
7W8H Sweet taste protein Brazzein mutant - D29K Deposited 2021-12-07	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–54（54 aa）	Mutation：D29K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0-1.5M NaCl 1M Na-Acetate pH4.5	Resolution 1.50 Å R-free 0.268
7W8H Sweet taste protein Brazzein mutant - D29K Deposited 2021-12-07	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–54（54 aa）	Mutation：D29K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0-1.5M NaCl 1M Na-Acetate pH4.5	Resolution 1.50 Å R-free 0.268
7W8H Sweet taste protein Brazzein mutant - D29K Deposited 2021-12-07	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–54（54 aa）	Mutation：D29K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0-1.5M NaCl 1M Na-Acetate pH4.5	Resolution 1.50 Å R-free 0.268
7W8H Sweet taste protein Brazzein mutant - D29K Deposited 2021-12-07	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 1–54（54 aa）	Mutation：D29K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0-1.5M NaCl 1M Na-Acetate pH4.5	Resolution 1.50 Å R-free 0.268
7W8H Sweet taste protein Brazzein mutant - D29K Deposited 2021-12-07	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 1–54（54 aa）	Mutation：D29K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；0-1.5M NaCl 1M Na-Acetate pH4.5	Resolution 1.50 Å R-free 0.268

10 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DEF_PENBA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–53； UniProt 2–54

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	2ly6
Deposition date deposition_date	2012-09-12
Structure title title	Refined solution structure of recombinant brazzein at low temperature
Keywords keywords	CYS-SAIL, brazzein, PLANT PROTEIN; PLANT PROTEIN
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	10.13 Å
Radius of gyration Rg (electron density) rg_electron	10.45 Å
Forward intensity I(0) i0	149999000.00
Molecular weight molecular_weight	95058.0 kDa
Excluded volume excluded_volume	115470 Å³
Envelope volume envelope_volume	10782 Å³
Hydration-shell volume shell_volume	8265 Å³
Envelope diameter envelope_diameter	38.5 Å
Shell Rg shell_rg	16.85 Å
Envelope Rg envelope_rg	12.11 Å
Shape Rg shape_rg	10.44 Å
Total Rg total_rg	10.64 Å
Total atoms total_atoms	12630
Residues n_residues	795
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	34.3 Å
Rg (real space) rg_real	10.12 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	1.5000e+08
I(0) uncertainty (real space) i0_real_error	1.6440e+06
Rg (reciprocal space) rg_reciprocal	10.12 Å
I(0) (reciprocal space) i0_reciprocal	150000000.0000
Solution quality estimate total_estimate	0.8809
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	11.7 Å
Skewness Skewness skewness	0.297
Kurtosis Kurtosis kurtosis	-0.365
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	62230.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; 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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2ly6a_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.7 — Scorpion toxin-like
Family Family family	g.3.7.5 — Plant defensins

CATH v4.4 (1 domains)

Domain ID domain_id	2ly6A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	30 — Defensin A-like
Homologous superfamily homologous superfamily	10 — Knottin, scorpion toxin-like

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8. Citations (1)

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Description description	Defensin-like protein
Molecular weight formula_weight	6380.2 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	12630

来源生物 organism	Pentadiplandra brazzeana
NCBI Class编号 ncbi_taxonomy_id	43545
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/ly/2ly6/2ly6.fit
pddf	/app/data/pr_computation/ly/2ly6/2ly6.pr.out
profile	/app/data/saxs_computation/ly/2ly6/2ly6.dat

Refined solution structure of recombinant brazzein at low temperature

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

Defensin-like protein

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

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)