2ww0

Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482

Method: X-RAY DIFFRACTION

▼

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

PUTATIVE ALPHA-1,2-MANNOSIDASE

BACTEROIDES THETAIOTAOMICRON

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL × 1 GLYCEROL × 5 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL × 1 GLYCEROL × 3 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL × 1 GLYCEROL × 3 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL × 1 GLYCEROL × 3 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL × 1 GLYCEROL × 2 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL × 1 GLYCEROL × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8A0N1_BACTN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–736； UniProt 20–755 Author chain B； PDBConstruct 1–736； UniProt 20–755 Author chain C； PDBConstruct 1–736； UniProt 20–755 Author chain D； PDBConstruct 1–736； UniProt 20–755 Author chain E； PDBConstruct 1–736； UniProt 20–755 Author chain F； PDBConstruct 1–736； UniProt 20–755 Author chain G； PDBConstruct 1–736； UniProt 20–755 Author chain H； PDBConstruct 1–736； UniProt 20–755

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	2ww0
Deposition date deposition_date	2009-10-21
Structure title title	Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482
Keywords keywords	HYDROLASE, GH92, BT3990, GLYCOSIDE HYDROLASE FAMILY 92; 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.

2ww0__assembly_8__model_1

Assembly 8 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ww0__assembly_8__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ww0__assembly_8__model_1 | P(r) · Pending

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

Rg（Guinier）	27.06 Å
Rg (electron density)	26.23 Å
Total Rg	27.06 Å
Atom count	5912
Residues	736
Excluded volume	104210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ww0__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ww0__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ww0__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2ww0__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2ww0__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2ww0__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2ww0__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2ww0__assembly_8__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	PUTATIVE ALPHA-1,2-MANNOSIDASE
Molecular weight formula_weight	85690.9 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	48426

KDWTQYVNPLMGSQSTFELSTGNTYPAIARPWGMNFWTPQTGKMGDGWQYTYTANKIRGFKQTHQPSPWINDYGQFSIMPIVGQPVFDEEKRASWFAHKGEVATPYYYKVYLAEHDIVTEMTPTERAVLFRFTFPENDHSYVVVDAFDKGSYIKIIPEENKIIGYTTRNSGGVPENFKNYFIIEFDKPFTYKATVENGNLQENVAEQTTDHAGAIIGFKTRKGEQVNARIASSFISFEQAAANMNELGKDNIEQLAQKGKDAWNQVLGKIEVEGGNLDQYRTFYSCLYRSLLFPRKFYELDANGQPIHYSPYNGQVLPGYMFTDTGFWDTFRCLFPLLNLMYPSVNKEMQEGLINTYLESGFFPEWASPGHRGCMVGNNSASILVDAYMKGVKVDDIKTLYEGLIHGTENVHPEVSSTGRLGYEYYNKLGYVPYDVKINENAARTLEYAYDDWCIYRLAKELKRPKKEISLFAKRAMNYKNLFDKESKLMRGRNEDGTFQSPFSPLKWGDAFTEGNSWHYTWSVFHDPQGLIDLMGGKEMFVTMMDSVFAVPPIFDDSYYGQVIHEIREMTVMNMGNYAHGNQPIQHMIYLYDYAGQPWKAQYWLRQVMDRMYTPGPDGYCGDEDNGQTSAWYVFSALGFYPVCPGTDEYVMGTPLFKKATLHFENGNSLVIDAPNNSTENFYIDSMSFNGADHTKNYLRHEDLFKGGTIKVDMSNRPNLNRGTKEEDMPYSFSKELEHHHHHH

Source Source

Source organism organism	BACTEROIDES THETAIOTAOMICRON
NCBI taxonomy ID ncbi_taxonomy_id	226186
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL
Molecular weight formula_weight	173.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	542

▼

6. Fold Classification (SCOP + CATH) 32 domains

CATH v4.4 (32 domains)

Domain ID domain_id	2ww0A01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww0A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww0A03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww0A04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

Domain ID domain_id	2ww0B01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww0B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww0B03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww0B04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

Domain ID domain_id	2ww0C01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww0C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww0C03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww0C04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

Domain ID domain_id	2ww0D01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww0D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww0D03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww0D04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

Domain ID domain_id	2ww0E01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww0E02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww0E03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww0E04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

Domain ID domain_id	2ww0F01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww0F02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww0F03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww0F04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

Domain ID domain_id	2ww0G01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww0G02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww0G03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww0G04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

Domain ID domain_id	2ww0H01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ww0H02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2080 — GH92 mannosidase fold
Homologous superfamily homologous superfamily	10 — GH92 mannosidase domain

Domain ID domain_id	2ww0H03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	60 — alpha-1,2-mannosidase

Domain ID domain_id	2ww0H04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1610 — Glycosyl hydrolase family fold
Homologous superfamily homologous superfamily	10 — alpha-1,2-mannosidases domains

▶

Unit-cell length a length_a	107.810 Å
Unit-cell length b length_b	151.960 Å
Unit-cell length c length_c	218.619 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.43 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	218.230 Å
R factor r_factor	0.1858
R_work r_work	0.1844
R_free r_free	0.2116

Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482

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

PUTATIVE ALPHA-1,2-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

2ww0__assembly_8__model_1

2ww0__assembly_8__model_1 | I(q)

2ww0__assembly_8__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) 32 domains

CATH v4.4 (32 domains)

7. Citations (1)

Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482

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

PUTATIVE ALPHA-1,2-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

2ww0__assembly_8__model_1

2ww0__assembly_8__model_1 | I(q)

2ww0__assembly_8__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) 32 domains

CATH v4.4 (32 domains)

7. Citations (1)