SAXSdb — 1e4i

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

BETA-GLUCOSIDASE

BACILLUS POLYMYXA

UniProt P22073

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 2–448	Mutation：YES	G2F 2-deoxy-2-fluoro-alpha-D-glucopyranose × 8 NFG 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside × 8	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；DROP: 10 MICROL PROTEIN (8 MG/ML)+ 5 MICROL PP(1M, PH=7)+5 MICROL INH (5MM) RESERVOIR: 1.3M PP, pH 7.00	Resolution 2.00 Å R-free 0.250

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 1E4I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BGA BETA-GLUCOSIDASE A FROM BACILLUS POLYMYXA Deposited 1997-04-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 2–448（447 aa） Chain B 2–448（447 aa） Chain C 2–448（447 aa） Chain D 2–448（447 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；PROTEIN WAS CRYSTALLIZED FROM 1.3 M NA/K PHOSPHATE, PH 8.3, 5 MICRO-L PROTEIN, 14 MG/ML, 5 MICRO-L RESERVOIR	Resolution 2.40 Å R-free 0.270
1BGG GLUCOSIDASE A FROM BACILLUS POLYMYXA COMPLEXED WITH GLUCONATE Deposited 1997-05-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–448（448 aa） Chain B 1–448（448 aa） Chain C 1–448（448 aa） Chain D 1–448（448 aa）	Not recorded	GCO D-gluconic acid × 6	X-RAY DIFFRACTION X-ray crystallization conditions co-crystallization；pH 8.3；COMPLEX WAS OBTAINED BY CO-CRYSTALLIZATION, 5 MICRO-L BGLA (14 MG/ML) / 5 MICRO-L 10MM LIGAND / 5 MICRO-L PP 1.3M, PH 8.3, co-crystallization	Resolution 2.30 Å R-free 0.250
1TR1 CRYSTAL STRUCTURE OF E96K MUTATED BETA-GLUCOSIDASE A FROM BACILLUS POLYMYXA, AN ENZYME WITH INCREASED THERMORESISTANCE Deposited 1998-03-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 2–448（447 aa） Chain B 2–448（447 aa） Chain C 2–448（447 aa） Chain D 2–448（447 aa）	Mutation：E96K Mutation：E96K Mutation：E96K Mutation：E96K	GOL GLYCEROL × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；pH 8.3	Resolution 2.20 Å R-free 0.282
1UYQ mutated b-glucosidase A from Paenibacillus polymyxa showing increased stability Deposited 2004-03-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 2–448（447 aa）	Mutation：YES	G2F 2-deoxy-2-fluoro-alpha-D-glucopyranose × 8 NFG 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；DROP: 1 MICROL PROTEIN (8 MG/ML)+ 1 MICROL PB(3M, PH=7)+1 MICROL INH (35MM) RESERVOIR: 1.3M PB, pH 7.00	Resolution 2.20 Å R-free 0.227
6QWI Structure of beta-glucosidase A from Paenibacillus polymyxa complexed with multivalent inhibitors. Deposited 2019-03-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–448（448 aa） Chain B 1–448（448 aa）	Not recorded	JJW (2~{S},3~{S},4~{R})-2-[[4-[4-(2-ethoxyethoxy)phenyl]-1,2,3-triazol-1-yl]methyl]pyrrolidine-3,4-diol × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；13% (v/v) PEG 3350, 0.2M sodium nitrate, 3% 2-Methyl-2,4-pentanediol (MPD) and 0.1 M BisTris propane, pH 7.5 and 0.56 mM 6-Cyclohexylhexyl beta-D-maltoside. Cryoprotectant mother liquor supplemented with 25% glycerol.	Resolution 2.85 Å R-free 0.231
6R4K Structure of beta-glucosidase A from Paenibacillus polymyxa complexed with a monovalent inhibitor Deposited 2019-03-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–448（448 aa） Chain B 1–448（448 aa）	Not recorded	JSK (2~{S},3~{S},4~{R})-2-[[4-[4-[2-[2-(2-azanylidenehydrazinyl)ethoxy]ethoxy]phenyl]-1,2,3-triazol-1-yl]methyl]pyrrolidine-3,4-diol × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；18% (v/v) PEG 3350, 0.2M sodium nitrate, 3% 2-Methyl-2,4-pentanediol (MPD), 0.1 M Bis-Tris propane, pH 7.5, and 5% n-Dodecyl beta-D-maltoside. Cryoprotectant mother liquor supplemented with 25% glycerol.	Resolution 2.13 Å R-free 0.241

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BGLA_PAEPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–447； UniProt 2–448

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	1e4i
Deposition date deposition_date	2000-07-06
Structure title title	2-deoxy-2-fluoro-beta-D-glucosyl/enzyme intermediate complex of the beta-glucosidase from Bacillus polymyxa
Keywords keywords	HYDROLASE, FAMILY 1 GLYCOSYL HYDROLASE, COVALENT ENZYME-GLYCOSIDE INTERMEDIATE, ALPHA/BETA BARREL; HYDROLASE
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	22.21 Å
Radius of gyration Rg (electron density) rg_electron	20.83 Å
Forward intensity I(0) i0	45673200.00
Molecular weight molecular_weight	52010.0 kDa
Excluded volume excluded_volume	64581 Å³
Envelope volume envelope_volume	71191 Å³
Hydration-shell volume shell_volume	27188 Å³
Envelope diameter envelope_diameter	70.9 Å
Shell Rg shell_rg	28.75 Å
Envelope Rg envelope_rg	21.14 Å
Shape Rg shape_rg	20.81 Å
Total Rg total_rg	21.75 Å
Total atoms total_atoms	3679
Residues n_residues	447
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	72.7 Å
Rg (real space) rg_real	22.01 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	4.5670e+07
I(0) uncertainty (real space) i0_real_error	4.9310e+05
Rg (reciprocal space) rg_reciprocal	22.05 Å
I(0) (reciprocal space) i0_reciprocal	45670000.0000
Solution quality estimate total_estimate	0.8019
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.2 Å
Skewness Skewness skewness	0.079
Kurtosis Kurtosis kurtosis	-0.495
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11570000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	BETA-GLUCOSIDASE
Molecular weight formula_weight	51566.6 kDa
EC 编号 ec_number	3.2.1.21
Mutation mutation	YES
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	3913

TIFQFPQDFMWGTATAAYQIEGAYQEDGRGLSIWDTFAHTPGKVFNGDNGNVACDSYHRYEEDIRLMKELGIRTYRFSVSWPRIFPNGDGEVNQKGLDYYHRVVDLLNDNGIEPFCTLYHWDLPQALQDAGGWGNRRTIQAFVQFAETMFREFHGKIQHWLTFNEPWCIAFLSNMLGVHAPGLTNLQTAIDVGHHLLVAHGLSVRRFRELGTSGQIGIAPNVSWAVPYSTSEEDKAACARTISLHSDWFLQPIYQGSYPQFLVDWFAEQGATVPIQDGDMDIIGEPIDMIGINYYSMSVNRFNPEAGFLQSEEINMGLPVTDIGWPVESRGLYEVLHYLQKYGNIDIYITENGACINDEVVNGKVQDDRRISYMQQHLVQVHRTIHDGLHVKGYMAWSLLDNFEWAEGYNMRFGMIHVDFRTQVRTPKQSYYWYRNVVSNNWLETRR

来源 Source

来源生物 organism	BACILLUS POLYMYXA
NCBI Class编号 ncbi_taxonomy_id	1406
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	2-deoxy-2-fluoro-alpha-D-glucopyranose
Molecular weight formula_weight	182.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside
Molecular weight formula_weight	348.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	234

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1e4ia_
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	1e4iA00
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	136.230 Å
Unit-cell length b length_b	136.230 Å
Unit-cell length c length_c	173.260 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	16

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2500

fit	/app/data/saxs_computation/e4/1e4i/1e4i.fit
pddf	/app/data/pr_computation/e4/1e4i/1e4i.pr.out
profile	/app/data/saxs_computation/e4/1e4i/1e4i.dat

2-deoxy-2-fluoro-beta-D-glucosyl/enzyme intermediate complex of the beta-glucosidase from Bacillus polymyxa

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

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