SAXSdb — 7w8h

▼

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 1–54	Mutation：D29K	No other associated polymer	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–54	Mutation：D29K	No other associated polymer	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–54	Mutation：D29K	No other associated polymer	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–54	Mutation：D29K	No other associated polymer	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
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 1–54	Mutation：D29K	No other associated polymer	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
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 1–54	Mutation：D29K	No other associated polymer	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
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 1–54	Mutation：D29K	No other associated polymer	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
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 1–54	Mutation：D29K	No other associated polymer	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

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 7W8H	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 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 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 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 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 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 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 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 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 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 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
2LY6 Refined solution structure of recombinant brazzein at low temperature Deposited 2012-09-12	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 2–54（53 aa）	Not recorded	No recorded non-water small molecule	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
2N66 NMR Structure of sweeter mutant (D40K) of sweet protein Brazzein, Deposited 2015-08-13	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：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 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）	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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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

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

View Construct and Data Evidence

UniProt name	DEF_PENBA
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–54； UniProt 1–54 Author chain B； PDBConstruct 1–54； UniProt 1–54 Author chain C； PDBConstruct 1–54； UniProt 1–54 Author chain E； PDBConstruct 1–54； UniProt 1–54 Author chain F； PDBConstruct 1–54； UniProt 1–54 Author chain G； PDBConstruct 1–54； UniProt 1–54 Author chain H； PDBConstruct 1–54； UniProt 1–54 Author chain D； PDBConstruct 1–54； UniProt 1–54

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7w8h
Deposition date deposition_date	2021-12-07
Structure title title	Sweet taste protein Brazzein mutant - D29K
Keywords keywords	Sweet taste protein, artficial sweetener, PLANT PROTEIN; PLANT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	28.23 Å
Radius of gyration Rg (electron density) rg_electron	27.54 Å
Forward intensity I(0) i0	50009300.00
Molecular weight molecular_weight	50756.0 kDa
Excluded volume excluded_volume	61857 Å³
Envelope volume envelope_volume	88445 Å³
Hydration-shell volume shell_volume	27733 Å³
Envelope diameter envelope_diameter	90.6 Å
Shell Rg shell_rg	33.57 Å
Envelope Rg envelope_rg	27.40 Å
Shape Rg shape_rg	27.53 Å
Total Rg total_rg	28.22 Å
Total atoms total_atoms	3502
Residues n_residues	423
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

▼

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

Maximum dimension Dmax dmax	86.7 Å
Rg (real space) rg_real	28.12 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	5.0010e+07
I(0) uncertainty (real space) i0_real_error	7.1610e+05
Rg (reciprocal space) rg_reciprocal	28.15 Å
I(0) (reciprocal space) i0_reciprocal	50010000.0000
Solution quality estimate total_estimate	0.9116
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.6 Å
Skewness Skewness skewness	0.132
Kurtosis Kurtosis kurtosis	-0.542
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1802000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.922

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Defensin-like protein
Molecular weight formula_weight	6525.5 kDa
Mutation mutation	D29K
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,E,F,G,H
Atom count atom_count	3812

MDKCKKVYENYPVSKCQLANQCNYDCKLKKHARSGECFYDEKRNLQCICDYCEY

来源 Source

来源生物 organism	Pentadiplandra brazzeana
NCBI Class编号 ncbi_taxonomy_id	43545
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Defensin-like protein
Molecular weight formula_weight	6511.4 kDa
Mutation mutation	D29K
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MDKCKKVYENYPVSKCQLANQCNYDCKLDKHARSGECFYDEKRNLQCICDYCEY

来源 Source

来源生物 organism	Pentadiplandra brazzeana
NCBI Class编号 ncbi_taxonomy_id	43545
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	310

▶

8. Citations (3)

▶

Unit-cell length a length_a	55.450 Å
Unit-cell length b length_b	55.450 Å
Unit-cell length c length_c	159.333 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	21

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	trigonal

Resolution resolution	1.501 Å
Low-resolution limit resolution_low	27.315 Å
R factor r_factor	0.2329
R_work r_work	0.2321
R_free r_free	0.2676

fit	/app/data/saxs_computation/w8/7w8h/7w8h.fit
pddf	/app/data/pr_computation/w8/7w8h/7w8h.pr.out
profile	/app/data/saxs_computation/w8/7w8h/7w8h.dat

Sweet taste protein Brazzein mutant - D29K

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)