SAXSdb — 3nke

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

protein ygbT

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	1,2-ETHANEDIOL × 4 SULFITE ION × 2 SULFATE ION × 5 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YGBT_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–200； UniProt 92–291 Author chain B； PDBConstruct 1–200； UniProt 92–291 Author chain C； PDBConstruct 1–200； UniProt 92–291

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	3nke
Deposition date deposition_date	2010-06-18
Structure title title	High resolution structure of the C-terminal domain CRISP-associated protein Cas1 from Escherichia coli str. K-12
Keywords keywords	CRISPR, Cas1, YgbT, Nuclease, DNA recombination, DNA repair, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

3nke__assembly_1__model_1

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

Download this curve (.dat)

3nke__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3nke__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.77 Å
Rg (electron density)	24.39 Å
Total Rg	25.31 Å
Atom count	4284
Residues	545
Excluded volume	76721 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3nke__assembly_1__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	protein ygbT
Molecular weight formula_weight	22118.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5145

GGARSDKLLYQAKLALDEDLRLKVVRKMFELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCISAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNPGEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPAPPEDAQPVAI

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SULFITE ION
Molecular weight formula_weight	80.1 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	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	768

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3nkea_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.79 — CRISPR associated protein Cas1-like
Superfamily Superfamily superfamily	e.79.1 — CRISPR associated protein Cas1-like
Family Family family	e.79.1.1 — CRISPR associated protein Cas1-like

Domain ID domain_id	d3nkeb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.79 — CRISPR associated protein Cas1-like
Superfamily Superfamily superfamily	e.79.1 — CRISPR associated protein Cas1-like
Family Family family	e.79.1.1 — CRISPR associated protein Cas1-like

Domain ID domain_id	d3nkec_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.79 — CRISPR associated protein Cas1-like
Superfamily Superfamily superfamily	e.79.1 — CRISPR associated protein Cas1-like
Family Family family	e.79.1.1 — CRISPR associated protein Cas1-like

CATH v4.4 (3 domains)

Domain ID domain_id	3nkeA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	920 — CRISPR-associated endonuclease Cas1, C-terminal domain

Domain ID domain_id	3nkeB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	920 — CRISPR-associated endonuclease Cas1, C-terminal domain

Domain ID domain_id	3nkeC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	920 — CRISPR-associated endonuclease Cas1, C-terminal domain

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Unit-cell length a length_a	53.709 Å
Unit-cell length b length_b	90.047 Å
Unit-cell length c length_c	121.876 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	12

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

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	33.200 Å
R factor r_factor	0.1778
R_work r_work	0.1766
R_free r_free	0.2007

High resolution structure of the C-terminal domain CRISP-associated protein Cas1 from Escherichia coli str. K-12

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

protein ygbT

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

3nke__assembly_1__model_1

3nke__assembly_1__model_1 | I(q)

3nke__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 (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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

High resolution structure of the C-terminal domain CRISP-associated protein Cas1 from Escherichia coli str. K-12

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

protein ygbT

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

3nke__assembly_1__model_1

3nke__assembly_1__model_1 | I(q)

3nke__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 (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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)