2ww1

Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 in complex with Thiomannobioside

Method: X-RAY DIFFRACTION

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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	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside × 1 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside × 1 water × 1	Consistent with protein count
3	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside × 1 water × 1	Consistent with protein count
4	Other combination	Monomer	Protein 1 其他Polymer 1	alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside × 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

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	2ww1
Deposition date deposition_date	2009-10-21
Structure title title	Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 in complex with Thiomannobioside
Keywords keywords	HYDROLASE, GLYCOSIDE HYDROLASE FAMILY 92, GH92, BT3990; 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.

2ww1__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ww1__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ww1__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	27.11 Å
Rg (electron density)	26.33 Å
Total Rg	27.20 Å
Atom count	5990
Residues	737
Excluded volume	105870 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ww1__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ww1__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ww1__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2ww1__assembly_4__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 (3)

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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	25408

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 branched

Description description	alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside
Molecular weight formula_weight	372.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1360

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	2ww1A01
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	2ww1A02
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	2ww1A03
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	2ww1A04
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	2ww1B01
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	2ww1B02
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	2ww1B03
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	2ww1B04
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	2ww1C01
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	2ww1C02
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	2ww1C03
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	2ww1C04
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	2ww1D01
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	2ww1D02
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	2ww1D03
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	2ww1D04
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

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Unit-cell length a length_a	66.240 Å
Unit-cell length b length_b	153.110 Å
Unit-cell length c length_c	185.210 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.37 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	185.160 Å
R factor r_factor	0.1890
R_work r_work	0.1875
R_free r_free	0.2182

Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 in complex with Thiomannobioside

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

2ww1__assembly_2__model_1

2ww1__assembly_2__model_1 | I(q)

2ww1__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482 in complex with Thiomannobioside

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

2ww1__assembly_2__model_1

2ww1__assembly_2__model_1 | I(q)

2ww1__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)