SAXSdb — 1byh

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 1 PDB declaration: monomeric	Entity 1：HYBRID × 1 Entity 2：beta-D-glucopyranose-(1-4)-beta-D-glucopyranose × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	CA CALCIUM ION × 1 NBU N-BUTANE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.80 Å

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	1byh
Deposition date deposition_date	1992-12-31
Structure title title	MOLECULAR AND ACTIVE-SITE STRUCTURE OF A BACILLUS (1-3,1-4)-BETA-GLUCANASE
Keywords keywords	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	17.27 Å
Radius of gyration Rg (electron density) rg_electron	15.95 Å
Forward intensity I(0) i0	10651100.00
Molecular weight molecular_weight	24353.0 kDa
Excluded volume excluded_volume	30345 Å³
Envelope volume envelope_volume	32322 Å³
Hydration-shell volume shell_volume	16661 Å³
Envelope diameter envelope_diameter	54.8 Å
Shell Rg shell_rg	22.43 Å
Envelope Rg envelope_rg	16.21 Å
Shape Rg shape_rg	15.93 Å
Total Rg total_rg	17.03 Å
Total atoms total_atoms	1725
Residues n_residues	214
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	57.9 Å
Rg (real space) rg_real	17.12 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	1.0650e+07
I(0) uncertainty (real space) i0_real_error	1.2430e+05
Rg (reciprocal space) rg_reciprocal	17.14 Å
I(0) (reciprocal space) i0_reciprocal	10650000.0000
Solution quality estimate total_estimate	0.8661
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.8 Å
Skewness Skewness skewness	0.057
Kurtosis Kurtosis kurtosis	-0.459
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2733000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 1.000

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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	HYBRID
Molecular weight formula_weight	23935.2 kDa
EC 编号 ec_number	3.2.1.73
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	1797

QTGGSFFEPFNSYNSGTWEKADGYSNGGVFNCTWRANNVNFTNDGKLKLGLTSSAYNKFDCAEYRSTNIYGYGLYEVSMKPAKNTGIVSSFFTYTGPAHGTQWDEIDIEFLGKDTTKVQFNYYTNGVGGHEKVISLGFDASKGFHTYAFDWQPGYIKWYVDGVLKHTATANIPSTPGKIMMNLWNGTGVDDWLGSYNGANPLYAEYDWVKYTSN

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630

Entity 2 Entity 2 branched

Description description	beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

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	1

Entity 4 Entity 4 non-polymer

Description description	N-BUTANE
Molecular weight formula_weight	58.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	72

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1byha_
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 (1 domains)

Domain ID domain_id	1byhA00
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 (2)

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Unit-cell length a length_a	64.320 Å
Unit-cell length b length_b	78.520 Å
Unit-cell length c length_c	39.300 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1680
R_work r_work	0.1680
R_free r_free	—

fit	/app/data/saxs_computation/by/1byh/1byh.fit
pddf	/app/data/pr_computation/by/1byh/1byh.pr.out
profile	/app/data/saxs_computation/by/1byh/1byh.dat

MOLECULAR AND ACTIVE-SITE STRUCTURE OF A BACILLUS (1-3,1-4)-BETA-GLUCANASE

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

Assembly Composition of the Current Entry

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution