SAXSdb — 6r4k

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

Beta-glucosidase A

Paenibacillus 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 1–448 Chain B； UniProt 1–448	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

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 6R4K	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
1E4I 2-deoxy-2-fluoro-beta-D-glucosyl/enzyme intermediate complex of the beta-glucosidase from Bacillus polymyxa Deposited 2000-07-06	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）	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
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 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）	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 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

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 1–448； UniProt 1–448 Author chain B； PDBConstruct 1–448； UniProt 1–448

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	6r4k
Deposition date deposition_date	2019-03-22
Structure title title	Structure of beta-glucosidase A from Paenibacillus polymyxa complexed with a monovalent inhibitor
Keywords keywords	HYDROLASE, BETA-GLUCOSIDASE, GLYCOSIDASE, CARBOHYDRATE, CARBOHYDRATE METABOLISM, POLISACCHARIDE DEGRADATION, COMPLEX, INHIBITOR; 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	32.39 Å
Radius of gyration Rg (electron density) rg_electron	31.76 Å
Forward intensity I(0) i0	171080000.00
Molecular weight molecular_weight	103860.0 kDa
Excluded volume excluded_volume	129210 Å³
Envelope volume envelope_volume	150960 Å³
Hydration-shell volume shell_volume	40195 Å³
Envelope diameter envelope_diameter	111.5 Å
Shell Rg shell_rg	38.14 Å
Envelope Rg envelope_rg	31.52 Å
Shape Rg shape_rg	31.76 Å
Total Rg total_rg	32.22 Å
Total atoms total_atoms	7350
Residues n_residues	896
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	105.3 Å
Rg (real space) rg_real	32.53 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	1.7110e+08
I(0) uncertainty (real space) i0_real_error	2.6120e+06
Rg (reciprocal space) rg_reciprocal	32.47 Å
I(0) (reciprocal space) i0_reciprocal	171100000.0000
Solution quality estimate total_estimate	0.8681
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	32.2 Å
Skewness Skewness skewness	0.437
Kurtosis Kurtosis kurtosis	-0.457
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	56270000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.790

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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	Beta-glucosidase A
Molecular weight formula_weight	51608.7 kDa
EC 编号 ec_number	3.2.1.21
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7808

MTIFQFPQDFMWGTATAAYQIEGAYQEDGRGLSIWDTFAHTPGKVFNGDNGNVACDSYHRYEEDIRLMKELGIRTYRFSVSWPRIFPNGDGEVNQKGLDYYHRVVDLLNDNGIEPFCTLYHWDLPQALQDAGGWGNRRTIQAFVQFAETMFREFHGKIQHWLTFNEPWCIAFLSNMLGVHAPGLTNLQTAIDVGHHLLVAHGLSVRRFRELGTSGQIGIAPNVSWAVPYSTSEEDKAACARTISLHSDWFLQPIYQGSYPQFLVDWFAEQGATVPIQDGDMDIIGEPIDMIGINYYSMSVNRFNPEAGFLQSEEINMGLPVTDIGWPVESRGLYEVLHYLQKYGNIDIYITENGACINDEVVNGKVQDDRRISYMQQHLVQVHRAIHDGLHVKGYMAWSLLDNFEWAEGYSMRFGIIHVDFRTQVRTPKESYYWYRKVVGNNWLETRR

来源 Source

来源生物 organism	Paenibacillus 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~{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
Molecular weight formula_weight	391.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	458

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6r4ka_
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

Domain ID domain_id	d6r4kb_
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 (2 domains)

Domain ID domain_id	6r4kA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	6r4kB01
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 (1)

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Unit-cell length a length_a	146.725 Å
Unit-cell length b length_b	146.725 Å
Unit-cell length c length_c	140.055 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	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.130 Å
Low-resolution limit resolution_low	48.646 Å
R factor r_factor	0.2175
R_work r_work	0.2159
R_free r_free	0.2413

fit	/app/data/saxs_computation/r4/6r4k/6r4k.fit
pddf	/app/data/pr_computation/r4/6r4k/6r4k.pr.out
profile	/app/data/saxs_computation/r4/6r4k/6r4k.dat

Structure of beta-glucosidase A from Paenibacillus polymyxa complexed with a monovalent inhibitor

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

Beta-glucosidase A

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