SAXSdb — 2wys

▼

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

ENDO-1,4-BETA-XYLANASE Y

CLOSTRIDIUM THERMOCELLUM

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-xylopyranose-(1-2)-beta-D-xylopyranose × 1 beta-D-xylopyranose × 1 CALCIUM ION × 3 PHOSPHATE ION × 1 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose × 1 CALCIUM ION × 1 PHOSPHATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XYNY_CLOTM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–540； UniProt 33–551 Author chain B； PDBConstruct 22–540； UniProt 33–551

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	2wys
Deposition date deposition_date	2009-11-20
Structure title title	High resolution crystallographic structure of the Clostridium thermocellum N-terminal endo-1,4-beta-D-xylanase 10B (Xyn10B) CBM22-1- GH10 modules complexed with xylohexaose
Keywords keywords	HYDROLASE, XYLAN DEGRADATION, CELLULOSOME, GLYCOSIDASE; 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.

2wys__assembly_1__model_1

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

Download this curve (.dat)

2wys__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wys__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.03 Å
Rg (electron density)	24.06 Å
Total Rg	24.84 Å
Atom count	4068
Residues	504
Excluded volume	71587 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wys__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2wys__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	ENDO-1,4-BETA-XYLANASE Y
Molecular weight formula_weight	60658.3 kDa
EC 编号 ec_number	3.2.1.8
Mutation mutation	YES
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	8545

MGSSHHHHHHSSGLVPRGSHMDYEVVHDTFEVNFDGWCNLGVDTYLTAVENEGNNGTRGMMVINRSSASDGAYSEKGFYLDGGVEYKYSVFVKHNGTGTETFKLSVSYLDSETEEENKEVIATKDVVAGEWTEISAKYKAPKTAVNITLSITTDSTVDFIFDDVTITRKGMAEANTVYAANAVLKDMYANYFRVGSVLNSGTVNNSSIKALILREFNSITCENEMKPDATLVQSGSTNTNIRVSLNRAASILNFCAQNNIAVRGHTLVWHSQTPQWFFKDNFQDNGNWVSQSVMDQRLESYIKNMFAEIQRQYPSLNLYAYDVVNAAVSDDANRTRYYGGAREPGYGNGRSPWVQIYGDNKFIEKAFTYARKYAPANCKLYYNDYNEYWDHKRDCIASICANLYNKGLLDGVGMQSHINADMNGFSGIQNYKAALQKYINIGCDVQITELDISTENGKFSLQQQADKYKAVFQAAVDINRTSSKGKVTAVCVWGPNDANTWLGSQNAPLLFNANNQPKPAYNAVASIIPQSEWGDGNNPA

Source Source

Source organism organism	CLOSTRIDIUM THERMOCELLUM
NCBI taxonomy ID ncbi_taxonomy_id	1515
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 branched

Description description	beta-D-xylopyranose-(1-2)-beta-D-xylopyranose
Molecular weight formula_weight	282.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
Molecular weight formula_weight	414.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	beta-D-xylopyranose
Molecular weight formula_weight	150.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	378

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2wysA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2wysA02
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	2wysB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2wysB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

▶

Unit-cell length a length_a	173.700 Å
Unit-cell length b length_b	173.700 Å
Unit-cell length c length_c	135.325 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	86.850 Å
R factor r_factor	0.1877
R_work r_work	0.1852
R_free r_free	0.2363

High resolution crystallographic structure of the Clostridium thermocellum N-terminal endo-1,4-beta-D-xylanase 10B (Xyn10B) CBM22-1- GH10 modules complexed with xylohexaose

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

ENDO-1,4-BETA-XYLANASE Y

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

2wys__assembly_1__model_1

2wys__assembly_1__model_1 | I(q)

2wys__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)

High resolution crystallographic structure of the Clostridium thermocellum N-terminal endo-1,4-beta-D-xylanase 10B (Xyn10B) CBM22-1- GH10 modules complexed with xylohexaose

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

ENDO-1,4-BETA-XYLANASE Y

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

2wys__assembly_1__model_1

2wys__assembly_1__model_1 | I(q)

2wys__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)