SAXSdb — 5nrk

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

Endoglucanase

Acetivibrio cellulolyticus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DocCel5: Type I dockerin repeat domain from A. cellulolyticus family 5 endoglucanase WP_010249057 S15I, I16N mutant × 2 CALCIUM ION × 6 THIOCYANATE ION × 3 GLYCEROL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9RPL0_9FIRM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–141； UniProt 1472–1611 Author chain C； PDBConstruct 2–141； UniProt 1472–1611

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	5nrk
Deposition date deposition_date	2017-04-24
Structure title title	Crystal structure of the sixth cohesin from Acetivibrio cellulolyticus' scaffoldin B in complex with Cel5 dockerin S15I, I16N mutant
Keywords keywords	cellulosome, cohesin, dockerin, type I cohesin-dockerin, Coh-Doc, protein-protein interaction, protein binding; PROTEIN BINDING
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.

5nrk__assembly_1__model_1

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

Download this curve (.dat)

5nrk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5nrk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.26 Å
Rg (electron density)	23.42 Å
Total Rg	24.30 Å
Atom count	3140
Residues	421
Excluded volume	56259 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5nrk__assembly_1__model_1`	tetrameric （4）	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	Endoglucanase
Molecular weight formula_weight	14747.4 kDa
EC 编号 ec_number	3.2.1.4
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3830

MQTGFNLSIDTVEGNPGSSVVVPVKLSGISKNGISTADFTVTYDATKLEYISGDAGSIVTNPGVNFGINKESDGKLKVLFLDYTMSTGYISTDGVFANLNFNIKSSAAIGSKAEVSISGTPTFGDSTLTPVVAKVTNGAVNLE

Source Source

Source organism organism	Acetivibrio cellulolyticus
NCBI taxonomy ID ncbi_taxonomy_id	35830
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DocCel5: Type I dockerin repeat domain from A. cellulolyticus family 5 endoglucanase WP_010249057 S15I, I16N mutant
Molecular weight formula_weight	7491.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

KPGDVDGNGSININDFALMRNYLLGNLKDFPAEDDIKAGDLNGDKSINSLDFAIMRMYLLGMITKFSV

Source Source

Source organism organism	Acetivibrio cellulolyticus
NCBI taxonomy ID ncbi_taxonomy_id	35830
Host organism host_organism	Escherichia coli BL21(DE3)

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	6

Entity 4 Entity 4 non-polymer

Description description	THIOCYANATE ION
Molecular weight formula_weight	58.1 kDa
Source method src_method	syn
Copy count entity_count	3

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	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	580

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d5nrka1
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	d5nrka2
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	d5nrkb_
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

Domain ID domain_id	d5nrkc1
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	d5nrkc2
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	d5nrkd_
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 (2 domains)

Domain ID domain_id	5nrkB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1330 — Type 1 dockerin domain
Homologous superfamily homologous superfamily	10 — Dockerin domain

Domain ID domain_id	5nrkD00
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	46.539 Å
Unit-cell length b length_b	79.809 Å
Unit-cell length c length_c	112.159 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	65.030 Å
R factor r_factor	0.1453
R_work r_work	0.1440
R_free r_free	0.1699

Crystal structure of the sixth cohesin from Acetivibrio cellulolyticus' scaffoldin B in complex with Cel5 dockerin S15I, I16N mutant

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

Endoglucanase

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

5nrk__assembly_1__model_1

5nrk__assembly_1__model_1 | I(q)

5nrk__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 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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the sixth cohesin from Acetivibrio cellulolyticus' scaffoldin B in complex with Cel5 dockerin S15I, I16N mutant

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

Endoglucanase

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

5nrk__assembly_1__model_1

5nrk__assembly_1__model_1 | I(q)

5nrk__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 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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

CATH v4.4 (2 domains)

7. Citations (1)