SAXSdb — 1u0a

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

Beta-glucanase

Paenibacillus macerans

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 40–237	Mutation：E105Q, E109Q	beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；293 K；25% (v/v) PEG Monomethyl Ether 550, 0.01 M Zinc Sulfate heptahydrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50	Resolution 1.64 Å R-free 0.197
2	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 40–237	Mutation：E105Q, E109Q	beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；293 K；25% (v/v) PEG Monomethyl Ether 550, 0.01 M Zinc Sulfate heptahydrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50	Resolution 1.64 Å R-free 0.197
3	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 40–237	Mutation：E105Q, E109Q	beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；293 K；25% (v/v) PEG Monomethyl Ether 550, 0.01 M Zinc Sulfate heptahydrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50	Resolution 1.64 Å R-free 0.197
4	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 40–237	Mutation：E105Q, E109Q	beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；293 K；25% (v/v) PEG Monomethyl Ether 550, 0.01 M Zinc Sulfate heptahydrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50	Resolution 1.64 Å R-free 0.197
5	Other combination Homooligomer Protein × 4 其他Polymer 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 40–237 Chain B； UniProt 40–237 Chain C； UniProt 40–237 Chain D； UniProt 40–237	Mutation：E105Q, E109Q	beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose × 4 CA CALCIUM ION × 4 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；293 K；25% (v/v) PEG Monomethyl Ether 550, 0.01 M Zinc Sulfate heptahydrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.50	Resolution 1.64 Å R-free 0.197

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 1U0A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AJK CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-84 Deposited 1997-05-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–237（131 aa）	Not recorded	CA CALCIUM ION × 1 PO4 PHOSPHATE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；SITTING DROP METHOD: A SOLUTION OF 12 MG OF PROTEIN PER ML IN 10 MM HEPES, PH 7.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 50 MM K-PHOSPHATE, PH 7.0 AND 20% (BY WEIGHT) PEG 8000, vapor diffusion - sitting drop	Resolution 1.80 Å R-free 0.219
1AJK CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-84 Deposited 1997-05-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 107–237（131 aa）	Not recorded	CA CALCIUM ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；SITTING DROP METHOD: A SOLUTION OF 12 MG OF PROTEIN PER ML IN 10 MM HEPES, PH 7.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 50 MM K-PHOSPHATE, PH 7.0 AND 20% (BY WEIGHT) PEG 8000, vapor diffusion - sitting drop	Resolution 1.80 Å R-free 0.219
1AJO CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-127 Deposited 1997-05-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–149（149 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；HANGING DROP METHOD: A SOLUTION OF 18 MG OF PROTEIN PER ML IN 20 MM TRIS/HCL, PH 9.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 0.1 M IMIDAZOLE, PH7.5,2 MM CA-CHLORIDE, 10% (BY WEIGHT) PEG 8000 AND 8% (BY VOL.) ETHYLENE GLYCOL., vapor diffusion - hanging drop	Resolution 2.07 Å R-free 0.235
1AJO CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-127 Deposited 1997-05-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–149（149 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；HANGING DROP METHOD: A SOLUTION OF 18 MG OF PROTEIN PER ML IN 20 MM TRIS/HCL, PH 9.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 0.1 M IMIDAZOLE, PH7.5,2 MM CA-CHLORIDE, 10% (BY WEIGHT) PEG 8000 AND 8% (BY VOL.) ETHYLENE GLYCOL., vapor diffusion - hanging drop	Resolution 2.07 Å R-free 0.235
1AXK ENGINEERED BACILLUS BIFUNCTIONAL ENZYME GLUXYN-1 Deposited 1997-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 82–237（156 aa） Fragment：FUSION OF 1,3-1,4-BETA-GLUCANASE DOMAIN AND 1,4-BETA-XYLANASE DOMAIN Chain B 82–237（156 aa） Fragment：FUSION OF 1,3-1,4-BETA-GLUCANASE DOMAIN AND 1,4-BETA-XYLANASE DOMAIN	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.10 Å R-free 0.224
1CPM NATIVE-LIKE IN VIVO FOLDING OF A CIRCULARLY PERMUTED JELLYROLL PROTEIN SHOWN BY CRYSTAL STRUCTURE ANALYSIS Deposited 1994-03-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 82–237（156 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1CPN NATIVE-LIKE IN VIVO FOLDING OF A CIRCULARLY PERMUTED JELLYROLL PROTEIN SHOWN BY CRYSTAL STRUCTURE ANALYSIS Deposited 1994-03-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 82–237（156 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1GLH CATION BINDING TO A BACILLUS (1,3-1,4)-BETA-GLUCANASE. GEOMETRY, AFFINITY AND EFFECT ON PROTEIN STABILITY Deposited 1994-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–239（214 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.225
1MAC CRYSTAL STRUCTURE AND SITE-DIRECTED MUTAGENESIS OF BACILLUS MACERANS ENDO-1,3-1,4-BETA-GLUCANASE Deposited 1994-12-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–239（212 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1MAC CRYSTAL STRUCTURE AND SITE-DIRECTED MUTAGENESIS OF BACILLUS MACERANS ENDO-1,3-1,4-BETA-GLUCANASE Deposited 1994-12-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–239（212 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
2AYH CRYSTAL AND MOLECULAR STRUCTURE AT 1.6 ANGSTROMS RESOLUTION OF THE HYBRID BACILLUS ENDO-1,3-1,4-BETA-D-GLUCAN 4-GLUCANOHYDROLASE H(A16-M) Deposited 1995-02-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–239（214 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å

8 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GUB_PAEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 17–214； UniProt 40–237 Author chain B； PDBConstruct 17–214； UniProt 40–237 Author chain C； PDBConstruct 17–214； UniProt 40–237 Author chain D； PDBConstruct 17–214； UniProt 40–237

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	1u0a
Deposition date deposition_date	2004-07-13
Structure title title	Crystal structure of the engineered beta-1,3-1,4-endoglucanase H(A16-M) in complex with beta-glucan tetrasaccharide
Keywords keywords	1, 3-1, 4-beta-glucanase, protein-carbohydrate interaction, active-site variant, jellyroll architecture, hydrolase; 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	32.21 Å
Radius of gyration Rg (electron density) rg_electron	31.00 Å
Forward intensity I(0) i0	154425000.00
Molecular weight molecular_weight	98680.0 kDa
Excluded volume excluded_volume	122650 Å³
Envelope volume envelope_volume	147470 Å³
Hydration-shell volume shell_volume	38552 Å³
Envelope diameter envelope_diameter	99.1 Å
Shell Rg shell_rg	39.19 Å
Envelope Rg envelope_rg	30.43 Å
Shape Rg shape_rg	31.02 Å
Total Rg total_rg	31.63 Å
Total atoms total_atoms	6975
Residues n_residues	856
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	94.3 Å
Rg (real space) rg_real	31.98 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	1.5440e+08
I(0) uncertainty (real space) i0_real_error	2.1740e+06
Rg (reciprocal space) rg_reciprocal	32.09 Å
I(0) (reciprocal space) i0_reciprocal	154400000.0000
Solution quality estimate total_estimate	0.9083
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.0 Å
Skewness Skewness skewness	-0.015
Kurtosis Kurtosis kurtosis	-0.750
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	87430000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.933

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Beta-glucanase
Molecular weight formula_weight	23933.3 kDa
EC 编号 ec_number	3.2.1.73
Mutation mutation	E105Q, E109Q
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8629

QTGGSFFEPFNSYNSGTWEKADGYSNGGVFNCTWRANNVNFTNDGKLKLGLTSSAYNKFDCAEYRSTNIYGYGLYEVSMKPAKNTGIVSSFFTYTGPAHGTQWDQIDIQFLGKDTTKVQFNYYTNGVGGHEKVISLGFDASKGFHTYAFDWQPGYIKWYVDGVLKHTATANIPSTPGKIMMNLWNGTGVDDWLGSYNGANPLYAEYDWVKYTSN

来源 Source

来源生物 organism	Paenibacillus macerans
NCBI Class编号 ncbi_taxonomy_id	44252
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose
Molecular weight formula_weight	666.6 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1596

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1u0aa_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.2 — Glycosyl hydrolases family 16

Domain ID domain_id	d1u0ab_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.2 — Glycosyl hydrolases family 16

Domain ID domain_id	d1u0ac_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.2 — Glycosyl hydrolases family 16

Domain ID domain_id	d1u0ad_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.2 — Glycosyl hydrolases family 16

CATH v4.4 (4 domains)

Domain ID domain_id	1u0aA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1u0aB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1u0aC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	1u0aD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

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8. Citations (1)

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Unit-cell length a length_a	75.769 Å
Unit-cell length b length_b	88.758 Å
Unit-cell length c length_c	154.795 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.640 Å
Low-resolution limit resolution_low	34.460 Å
R factor r_factor	0.1640
R_work r_work	0.1610
R_free r_free	0.1970

fit	/app/data/saxs_computation/u0/1u0a/1u0a.fit
pddf	/app/data/pr_computation/u0/1u0a/1u0a.pr.out
profile	/app/data/saxs_computation/u0/1u0a/1u0a.dat

Crystal structure of the engineered beta-1,3-1,4-endoglucanase H(A16-M) in complex with beta-glucan tetrasaccharide

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

Beta-glucanase

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