1cbg

THE CRYSTAL STRUCTURE OF A CYANOGENIC BETA-GLUCOSIDASE FROM WHITE CLOVER (TRIFOLIUM REPENS L.), A FAMILY 1 GLYCOSYL-HYDROLASE

Method: X-RAY DIFFRACTION D_max: 69.1 Å Quality: EXCELLENT

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

CYANOGENIC BETA-GLUCOSIDASE

OrganismNot specified

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 12–412	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.15 Å R-free 0.247

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	BGLT_TRIRP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–401； UniProt 12–412

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	1cbg
Deposition date deposition_date	1995-07-31
Structure title title	THE CRYSTAL STRUCTURE OF A CYANOGENIC BETA-GLUCOSIDASE FROM WHITE CLOVER (TRIFOLIUM REPENS L.), A FAMILY 1 GLYCOSYL-HYDROLASE
Keywords keywords	CYANOGENIC BETA-GLUCOSIDASE, HYDROLASE (O-GLYCOSYL); HYDROLASE (O-GLYCOSYL)
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	23.21 Å
Radius of gyration Rg (electron density) rg_electron	21.88 Å
Forward intensity I(0) i0	50089900.00
Molecular weight molecular_weight	56335.0 kDa
Excluded volume excluded_volume	70868 Å³
Envelope volume envelope_volume	82026 Å³
Hydration-shell volume shell_volume	29681 Å³
Envelope diameter envelope_diameter	71.1 Å
Shell Rg shell_rg	30.15 Å
Envelope Rg envelope_rg	22.24 Å
Shape Rg shape_rg	21.83 Å
Total Rg total_rg	22.99 Å
Total atoms total_atoms	3993
Residues n_residues	490
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	69.1 Å
Rg (real space) rg_real	23.02 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	5.0090e+07
I(0) uncertainty (real space) i0_real_error	5.7640e+05
Rg (reciprocal space) rg_reciprocal	23.07 Å
I(0) (reciprocal space) i0_reciprocal	50090000.0000
Solution quality estimate total_estimate	0.9050
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.8 Å
Skewness Skewness skewness	0.079
Kurtosis Kurtosis kurtosis	-0.486
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11500000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.982

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cbga_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.4 — Family 1 of glycosyl hydrolase

CATH v4.4 (1 domains)

Domain ID domain_id	1cbgA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

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8. Citations (2)

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Unit-cell length a length_a	70.326 Å
Unit-cell length b length_b	70.326 Å
Unit-cell length c length_c	249.096 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	9.000 Å
R factor r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2470

Description description	CYANOGENIC BETA-GLUCOSIDASE
Molecular weight formula_weight	56419.7 kDa
EC 编号 ec_number	3.2.1.21
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4429

THE CRYSTAL STRUCTURE OF A CYANOGENIC BETA-GLUCOSIDASE FROM WHITE CLOVER (TRIFOLIUM REPENS L.), A FAMILY 1 GLYCOSYL-HYDROLASE

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

CYANOGENIC BETA-GLUCOSIDASE

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	436

fit	/app/data/saxs_computation/cb/1cbg/1cbg.fit
pddf	/app/data/pr_computation/cb/1cbg/1cbg.pr.out
profile	/app/data/saxs_computation/cb/1cbg/1cbg.dat