SAXSdb — 5ds5

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

CRISPR-associated endonuclease Cas1

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	CRISPR-associated endoribonuclease Cas2 × 2 （P45956） DNA (28-MER) × 1 DNA (28-MER) × 1 MAGNESIUM ION × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAS1_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–306； UniProt 1–305 Author chain B； PDBConstruct 2–306； UniProt 1–305 Author chain C； PDBConstruct 2–306； UniProt 1–305 Author chain D； PDBConstruct 2–306； UniProt 1–305

CRISPR-associated endoribonuclease Cas2

Escherichia coli (strain K12)

UniProt P45956

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	CRISPR-associated endonuclease Cas1 × 4 （Q46896） DNA (28-MER) × 1 DNA (28-MER) × 1 MAGNESIUM ION × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAS2_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 2–95； UniProt 1–94 Author chain F； PDBConstruct 2–95； UniProt 1–94

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	5ds5
Deposition date deposition_date	2015-09-16
Structure title title	Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA and Mg
Keywords keywords	;Adaptive Immunity, CRISPR-Associated Proteins, CRISPR-Cas Systems, Clustered Regularly Interspaced Short Palindromic Repeats, Integrases, Endodeoxyribonucleases, Endonucleases, DNA binding protein, Hydrolase-DNA complex ;; Hydrolase/DNA
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.

5ds5__assembly_1__model_1

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

Download this curve (.dat)

5ds5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ds5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.86 Å
Rg (electron density)	41.03 Å
Total Rg	41.19 Å
Atom count	10719
Residues	1298
Excluded volume	189120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ds5__assembly_1__model_1`	octameric （8）	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	CRISPR-associated endonuclease Cas1
Molecular weight formula_weight	33322.5 kDa
EC 编号 ec_number	3.1.-.-
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	10719

SMTWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRVSHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMFELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCISAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNPGEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPAPPEDAQPVAIPLPVSLGDAGHRSS

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	CRISPR-associated endoribonuclease Cas2
Molecular weight formula_weight	11684.5 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

MMSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMAWATNTETGFEFQTFGLNRRTPVDLDGLRLVSFLPVGSSENLYFQ

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	DNA (28-MER)
Molecular weight formula_weight	8680.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

AAACACCAGAACGAGTAGTAAATTGGGC

Entity 4 Entity 4 polymer

Description description	DNA (28-MER)
Molecular weight formula_weight	8534.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

ATTTACTACTCGTTCTGGTGTTTCTCGT

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	5

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5ds5A01
Class class	3 — Alpha Beta
Architecture architecture	100 — Ribosomal Protein L15; Chain: K; domain 2
Topology topology	10 — Ribosomal Protein L15; Chain: K; domain 2
Homologous superfamily homologous superfamily	20 — CRISPR-associated endonuclease Cas1, N-terminal domain

Domain ID domain_id	5ds5A02
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	5ds5B01
Class class	3 — Alpha Beta
Architecture architecture	100 — Ribosomal Protein L15; Chain: K; domain 2
Topology topology	10 — Ribosomal Protein L15; Chain: K; domain 2
Homologous superfamily homologous superfamily	20 — CRISPR-associated endonuclease Cas1, N-terminal domain

Domain ID domain_id	5ds5B02
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	5ds5C01
Class class	3 — Alpha Beta
Architecture architecture	100 — Ribosomal Protein L15; Chain: K; domain 2
Topology topology	10 — Ribosomal Protein L15; Chain: K; domain 2
Homologous superfamily homologous superfamily	20 — CRISPR-associated endonuclease Cas1, N-terminal domain

Domain ID domain_id	5ds5C02
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	5ds5D01
Class class	3 — Alpha Beta
Architecture architecture	100 — Ribosomal Protein L15; Chain: K; domain 2
Topology topology	10 — Ribosomal Protein L15; Chain: K; domain 2
Homologous superfamily homologous superfamily	20 — CRISPR-associated endonuclease Cas1, N-terminal domain

Domain ID domain_id	5ds5D02
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	75.656 Å
Unit-cell length b length_b	165.928 Å
Unit-cell length c length_c	167.258 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	16

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

Resolution resolution	2.951 Å
Low-resolution limit resolution_low	46.475 Å
R factor r_factor	0.2348
R_work r_work	0.2335
R_free r_free	0.2564

Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA and Mg

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

CRISPR-associated endonuclease Cas1

State in the Current Structure

Other States of the Same Protein in the Database

CRISPR-associated endoribonuclease Cas2

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

5ds5__assembly_1__model_1

5ds5__assembly_1__model_1 | I(q)

5ds5__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA and Mg

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

CRISPR-associated endonuclease Cas1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CRISPR-associated endoribonuclease Cas2

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

5ds5__assembly_1__model_1

5ds5__assembly_1__model_1 | I(q)

5ds5__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)