SAXSdb — 1wky

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

endo-beta-1,4-Mannanase

Bacillus sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 2 CALCIUM ION × 1 SODIUM ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4W8M3_9BACI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–464； UniProt 30–490

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	1wky
Deposition date deposition_date	2004-06-15
Structure title title	Crystal structure of alkaline mannanase from Bacillus sp. strain JAMB-602: catalytic domain and its Carbohydrate Binding Module
Keywords keywords	TIM BARREL, CATALYTIC DOMAIN, CBM, hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1wky__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1wky__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wky__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	23.79 Å
Rg (electron density)	22.87 Å
Total Rg	23.66 Å
Atom count	3468
Residues	446
Excluded volume	60559 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wky__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	endo-beta-1,4-Mannanase
Molecular weight formula_weight	51032.6 kDa
EC 编号 ec_number	3.2.1.78
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	3883

GRPANANSGFYVSGTTLYDANGNPFVMRGINHGHAWYKDQATTAIEGIANTGANTVRIVLSDGGQWTKDDIQTVRNLISLAEDNNLVAVLEVHDATGYDSIASLNRAVDYWIEMRSALIGKEDTVIINIANEWFGSWDGAAWADGYKQAIPRLRNAGLNNTLMIDAAGWGQFPQSIHDYGREVFNADPQRNTMFSIHMYEYAGGNASQVRTNIDRVLNQDLALVIGEFGHRHTNGDVDESTIMSYSEQRGVGWLAWSWKGNGPEWEYLDLSNDWAGNNLTAWGNTIVNGPYGLRETSKLSTVFTGGGSDGRTSPTTLYDFEESTQGWTGSSLSRGPWTVTEWSSKGNHSLKADIQMSSNSQHYLHVIQNRSLQQNSRIQATVKHANWGSVGNGMTARLYVKTGHGYTWYSGSFVPINGSSGTTLSLDLSNVQNLSQVREIGVQFQSESNSSGQTSIYIDNVIVE

Source Source

Source organism organism	Bacillus sp.
NCBI taxonomy ID ncbi_taxonomy_id	244966
Host organism host_organism	Bacillus subtilis

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

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	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	376

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1wkya1
Class class	b — All beta proteins
Fold Fold fold	b.18 — Galactose-binding domain-like
Superfamily Superfamily superfamily	b.18.1 — Galactose-binding domain-like
Family Family family	b.18.1.31 — beta-mannanase CBM

Domain ID domain_id	d1wkya2
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.1.8.3 — beta-glycanases

CATH v4.4 (2 domains)

Domain ID domain_id	1wkyA01
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	1wkyA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

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Unit-cell length a length_a	70.682 Å
Unit-cell length b length_b	79.480 Å
Unit-cell length c length_c	80.418 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	1.650 Å
Low-resolution limit resolution_low	44.150 Å
R factor r_factor	0.1780
R_work r_work	0.1780
R_free r_free	0.2000

Crystal structure of alkaline mannanase from Bacillus sp. strain JAMB-602: catalytic domain and its Carbohydrate Binding Module

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

endo-beta-1,4-Mannanase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1wky__assembly_1__model_1

1wky__assembly_1__model_1 | I(q)

1wky__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of alkaline mannanase from Bacillus sp. strain JAMB-602: catalytic domain and its Carbohydrate Binding Module

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

endo-beta-1,4-Mannanase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1wky__assembly_1__model_1

1wky__assembly_1__model_1 | I(q)

1wky__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)