SAXSdb — 1odz

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

Mannan endo-1,4-beta-mannosidase

Cellvibrio japonicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose × 1 ZINC ION × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 SODIUM ION × 1 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose × 1 ZINC ION × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 SODIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MANA_CELJU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–386； UniProt 39–423 Author chain B； PDBConstruct 2–386； UniProt 39–423

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	1odz
Deposition date deposition_date	2003-03-17
Structure title title	Expansion of the glycosynthase repertoire to produce defined manno-oligosaccharides
Keywords keywords	HYDROLASE, MANNANASE, FAMILY 26, GLYCOSIDE-HYDROLASE, GLYCOSYNTHASE, MANNO-OLIGOSACCHARIDE; 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.

1odz__assembly_1__model_1

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

Download this curve (.dat)

1odz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1odz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.78 Å
Rg (electron density)	19.47 Å
Total Rg	20.52 Å
Atom count	3066
Residues	379
Excluded volume	54050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1odz__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1odz__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	Mannan endo-1,4-beta-mannosidase
Molecular weight formula_weight	43675.6 kDa
EC 编号 ec_number	3.2.1.78
Mutation mutation	E320G
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	7200

MRADVKPVTVKLVDSQATMETRSLFAFMQEQRRHSIMFGHQHETTQGLTITRTDGTQSDTFNAVGDFAAVYGWDTLSIVAPKAEGDIVAQVKKAYARGGIITVSSHFDNPKTDTQKGVWPVGTSWDQTPAVVDSLPGGAYNPVLNGYLDQVAEWANNLKDEQGRLIPVIFRLYHENTGSWFWWGDKQSTPEQYKQLFRYSVEYLRDVKGVRNFLYAYSPNNFWDVTEANYLERYPGDEWVDVLGFDTYGPVADNADWFRNVVANAALVARMAEARGKIPVISGIGIRAPDIEAGLYDNQWYRKLISGLKADPDAREIAFLLVWRNAPQGVPGPNGTQVPHYWVPANRPENINNGTLEDFQAFYADEFTAFNRDIEQVYQRPTLIVK

Source Source

Source organism organism	Cellvibrio japonicus
NCBI taxonomy ID ncbi_taxonomy_id	155077
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 branched

Description description	beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1033

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1odza_
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

Domain ID domain_id	d1odzb_
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	1odzA00
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	1odzB00
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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Unit-cell length a length_a	131.855 Å
Unit-cell length b length_b	131.855 Å
Unit-cell length c length_c	54.268 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	8

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1520
R_work r_work	0.1510
R_free r_free	0.1770

Expansion of the glycosynthase repertoire to produce defined manno-oligosaccharides

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

Mannan endo-1,4-beta-mannosidase

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

1odz__assembly_1__model_1

1odz__assembly_1__model_1 | I(q)

1odz__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Expansion of the glycosynthase repertoire to produce defined manno-oligosaccharides

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

Mannan endo-1,4-beta-mannosidase

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

1odz__assembly_1__model_1

1odz__assembly_1__model_1 | I(q)

1odz__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)