SAXSdb — 5oll

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

Gurmarin

Gymnema sylvestre

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–35	Not recorded	NI NICKEL (II) ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；100 mM MES, 5 mM MgCl2, 5 mM CaCl2, 50 mM CdCl2, 50 mM NiCl2 and 12% (w/v) PEG 3350	Resolution 1.45 Å R-free 0.191

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 5OLL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C4E GURMARIN FROM GYMNEMA SYLVESTRE Deposited 1999-07-27	Different mutation/modification Different oligomeric state 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 1–35（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 2.9；298 K；Pressure ATMOSPHERIC	Resolution not provided
1GUR GURMARIN, A SWEET TASTE-SUPPRESSING POLYPEPTIDE, NMR, 10 STRUCTURES Deposited 1996-03-12	Different construct Different mutation/modification Different oligomeric state 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 2–35（34 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GUR_GYMSY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–35； UniProt 1–35

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	5oll
Deposition date deposition_date	2017-07-28
Structure title title	Crystal structure of gurmarin, a sweet taste suppressing polypeptide
Keywords keywords	Gurmarin, sweet, taste, knottin, GPCR, inhibitor, plant protein; PLANT PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	10.74 Å
Radius of gyration Rg (electron density) rg_electron	9.79 Å
Forward intensity I(0) i0	569667.00
Molecular weight molecular_weight	4407.0 kDa
Excluded volume excluded_volume	5350 Å³
Envelope volume envelope_volume	6126 Å³
Hydration-shell volume shell_volume	5841 Å³
Envelope diameter envelope_diameter	36.4 Å
Shell Rg shell_rg	14.42 Å
Envelope Rg envelope_rg	10.28 Å
Shape Rg shape_rg	9.80 Å
Total Rg total_rg	11.22 Å
Total atoms total_atoms	296
Residues n_residues	35
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	37.8 Å
Rg (real space) rg_real	10.75 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	5.6970e+05
I(0) uncertainty (real space) i0_real_error	6.1700e+03
Rg (reciprocal space) rg_reciprocal	10.75 Å
I(0) (reciprocal space) i0_reciprocal	569700.0000
Solution quality estimate total_estimate	0.8583
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	12.4 Å
Skewness Skewness skewness	0.394
Kurtosis Kurtosis kurtosis	-0.090
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	94620.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.770; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.928

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Gurmarin
Molecular weight formula_weight	4239.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	367

EQCVKKDELCIPYYLDCCEPLECKKVNWWDHKCIG

来源 Source

来源生物 organism	Gymnema sylvestre
通用名 common_name	Gurmar
NCBI Class编号 ncbi_taxonomy_id	4068
宿主生物 host_organism	Komagataella phaffii GS115

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5olla_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.4 — Gurmarin-like
Family Family family	g.3.4.1 — Gurmarin, a sweet taste-suppressing polypeptide

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8. Citations (1)

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Unit-cell length a length_a	53.650 Å
Unit-cell length b length_b	53.650 Å
Unit-cell length c length_c	38.110 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	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.1900
R_work r_work	0.1900
R_free r_free	0.1910

fit	/app/data/saxs_computation/ol/5oll/5oll.fit
pddf	/app/data/pr_computation/ol/5oll/5oll.pr.out
profile	/app/data/saxs_computation/ol/5oll/5oll.dat

Crystal structure of gurmarin, a sweet taste suppressing polypeptide

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

Gurmarin

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