5m0y

Crystal Structure of the CohScaA-XDocCipB type II complex from Clostridium thermocellum at 1.5Angstrom resolution

Method: X-RAY DIFFRACTION

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

Ig domain protein group 2 domain protein

Clostridium thermocellum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Cellulosome anchoring protein cohesin region × 1 （A3DF10） CALCIUM ION × 2 SULFATE ION × 1 GLYCEROL × 1 1,2-ETHANEDIOL × 6 TRIETHYLENE GLYCOL × 1 HEXAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A3DGE8_CLOTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 2–164； UniProt 2015–2177

Cellulosome anchoring protein cohesin region

Clostridium thermocellum

UniProt A3DF10

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ig domain protein group 2 domain protein × 1 （A3DGE8） CALCIUM ION × 2 SULFATE ION × 1 GLYCEROL × 1 1,2-ETHANEDIOL × 6 TRIETHYLENE GLYCOL × 1 HEXAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A3DF10_CLOTH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 4–178； UniProt 27–201

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	5m0y
Deposition date deposition_date	2016-10-06
Structure title title	Crystal Structure of the CohScaA-XDocCipB type II complex from Clostridium thermocellum at 1.5Angstrom resolution
Keywords keywords	cellulosome, plant cell wall degradation, protein-protein interaction, cohesin-dockerin complex, cell adhesion; CELL ADHESION
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.

5m0y__assembly_1__model_1

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

Download this curve (.dat)

5m0y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5m0y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.17 Å
Rg (electron density)	23.55 Å
Total Rg	24.38 Å
Atom count	2635
Residues	331
Excluded volume	47305 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5m0y__assembly_1__model_1`	dimeric （2）	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 (9)

Entity 1 Entity 1 polymer

Description description	Ig domain protein group 2 domain protein
Molecular weight formula_weight	18245.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	2854

MNNDSTDKTTVSGYISVDFDYPPESESKIKSGFNVKVAGTELSTKTDEKGYFEISGIPGDMREFTLEISKRNYLKRNVTVNGTGKLVVSTEDNPLILWAGDVERKGVQDNAINMVDVMEISKVFGTRAGDEEYVAELDLNMDGAINLFDIAIVIRHFNALPSRY

Source Source

Source organism organism	Clostridium thermocellum
NCBI taxonomy ID ncbi_taxonomy_id	203119
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cellulosome anchoring protein cohesin region
Molecular weight formula_weight	20507.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MASRADKASSIELKFDRNKGEVGDILIGTVRINNIKNFAGFQVNIVYDPKVLMAVDPETGKEFTSSTFPPGRTVLKNNAYGPIQIADNDPEKGILNFALAYSYIAGYKETGVTEESGIIAKIGFKILQKKSTAVKFQDTLSMPGAILGTQLFDWDGEVITGYEVIQPDVLSLGDEPYEVEHHHHHH

Source Source

Source organism organism	Clostridium thermocellum
NCBI taxonomy ID ncbi_taxonomy_id	203119
Host organism host_organism	Escherichia coli

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	2

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	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	HEXAETHYLENE GLYCOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	183

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5m0ya1
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.2 — Carbohydrate-binding domain
Family Family family	b.2.2.2 — Cellulose-binding domain family III

Domain ID domain_id	d5m0ya2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5m0yb1
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.2 — Carboxypeptidase regulatory domain-like
Family Family family	b.3.2.0 — automated matches

Domain ID domain_id	d5m0yb2
Class class	a — All alpha proteins
Fold Fold fold	a.139 — Type I dockerin domain
Superfamily Superfamily superfamily	a.139.1 — Type I dockerin domain
Family Family family	a.139.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	5m0yA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	680 —

Domain ID domain_id	5m0yB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1120 — Carboxypeptidase-like, regulatory domain

Domain ID domain_id	5m0yB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1330 — Type 1 dockerin domain
Homologous superfamily homologous superfamily	10 — Dockerin domain

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Unit-cell length a length_a	43.408 Å
Unit-cell length b length_b	63.741 Å
Unit-cell length c length_c	141.196 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	47.300 Å
R factor r_factor	0.1912
R_work r_work	0.1905
R_free r_free	0.2032

Crystal Structure of the CohScaA-XDocCipB type II complex from Clostridium thermocellum at 1.5Angstrom resolution

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

Ig domain protein group 2 domain protein

State in the Current Structure

Other States of the Same Protein in the Database

Cellulosome anchoring protein cohesin region

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

5m0y__assembly_1__model_1

5m0y__assembly_1__model_1 | I(q)

5m0y__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal Structure of the CohScaA-XDocCipB type II complex from Clostridium thermocellum at 1.5Angstrom resolution

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

Ig domain protein group 2 domain protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cellulosome anchoring protein cohesin region

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

5m0y__assembly_1__model_1

5m0y__assembly_1__model_1 | I(q)

5m0y__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)