SAXSdb — 3azz

▼

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

Laminarinase

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	D-glucono-1,5-lactone × 1 CALCIUM ION × 1 SULFATE ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	D-glucono-1,5-lactone × 1 CALCIUM ION × 1 SULFATE ION × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	D-glucono-1,5-lactone × 1 CALCIUM ION × 1 SULFATE ION × 2 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 SULFATE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WXN1_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–264； UniProt 204–466 Author chain B； PDBConstruct 2–264； UniProt 204–466 Author chain C； PDBConstruct 2–264； UniProt 204–466 Author chain D； PDBConstruct 2–264； UniProt 204–466

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3azz
Deposition date deposition_date	2011-06-03
Structure title title	Crystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8 in complex with gluconolactone
Keywords keywords	beta-jelly roll fold, Glycosyl hydrolase family 16, Laminarinase, Endo-1, 3-beta-glucanase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3azz__assembly_1__model_1

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

Download this curve (.dat)

3azz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3azz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.74 Å
Rg (electron density)	17.37 Å
Total Rg	18.34 Å
Atom count	2048
Residues	250
Excluded volume	36027 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3azz__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3azz__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3azz__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3azz__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Laminarinase
Molecular weight formula_weight	31236.4 kDa
EC 编号 ec_number	3.2.1.39
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	8792

MEDEDKVEDWQLVWSQEFDDGVIDPNIWNFEIGNGHAKGIPGWGNGELEYYTDENAFVENGCLVIEARKEQVSDEYGTYDYTSARMTTEGKFEIKYGKIEIRAKLPKGKGIWPALWMLGNNIGEVGWPTCGEIDIMEMLGHDTRTVYGTAHGPGYSGGASIGVAYHLPEGVPDFSEDFHIFSIEWDEDEVEWYVDGQLYHVLSKDELAELGLEWVFDHPFFLILNVAVGGYWPGYPDETTQFPQRMYIDYIRVYKDMNPETITGVEHHHHHH

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	D-glucono-1,5-lactone
Molecular weight formula_weight	178.1 kDa
Source method src_method	man
Copy count entity_count	3

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	585

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3azza_
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	d3azzb_
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	d3azzc_
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	d3azzd_
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	3azzA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3azzB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3azzC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3azzD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

▶

Unit-cell length a length_a	106.990 Å
Unit-cell length b length_b	120.232 Å
Unit-cell length c length_c	120.995 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	1.810 Å
Low-resolution limit resolution_low	26.400 Å
R factor r_factor	0.1713
R_work r_work	0.1697
R_free r_free	0.2002

Crystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8 in complex with gluconolactone

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

Laminarinase

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

3azz__assembly_1__model_1

3azz__assembly_1__model_1 | I(q)

3azz__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8 in complex with gluconolactone

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

Laminarinase

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

3azz__assembly_1__model_1

3azz__assembly_1__model_1 | I(q)

3azz__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)