SAXSdb — 5dlj

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

CRISPR-associated endonuclease Cas1

Escherichia coli 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	39-mer DNA N1-F × 1 39-mer DNA N1-R × 1 CRISPR-associated endoribonuclease Cas2 × 2 （P45956） water × 8	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 1–280； UniProt 2–281 Author chain B； PDBConstruct 1–280； UniProt 2–281 Author chain C； PDBConstruct 1–280； UniProt 2–281 Author chain D； PDBConstruct 1–280； UniProt 2–281

CRISPR-associated endoribonuclease Cas2

Escherichia coli 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） 39-mer DNA N1-F × 1 39-mer DNA N1-R × 1 water × 8	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	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–78； UniProt 1–78 Author chain F； PDBConstruct 1–78； UniProt 1–78

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	5dlj
Deposition date deposition_date	2015-09-05
Structure title title	Crystal Structure of Cas-DNA-N1 complex
Keywords keywords	protein-DNA complex, 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.

5dlj__assembly_1__model_1

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

Download this curve (.dat)

5dlj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dlj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.21 Å
Rg (electron density)	42.12 Å
Total Rg	42.35 Å
Atom count	11239
Residues	1328
Excluded volume	197210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dlj__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	30709.6 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	D,C,A,B
Atom count atom_count	11444

TWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRVSHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMFELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCISAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNPGEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPA

Source Source

Source organism organism	Escherichia coli K12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	39-mer DNA N1-F
Molecular weight formula_weight	11949.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

TTTTTTCGTAGCTGAGGGCCTCAGCTACGTTTTTTTTTT

Entity 3 Entity 3 polymer

Description description	39-mer DNA N1-R
Molecular weight formula_weight	11909.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

TTTTTTCGTAGCTGAGGCCCTCAGCTACGTTTTTTTTTT

Entity 4 Entity 4 polymer

Description description	CRISPR-associated endoribonuclease Cas2
Molecular weight formula_weight	8803.2 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	F,E

MSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMAWATNTETGFEFQTFGLNRR

Source Source

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	205

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5dljA01
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	5dljA02
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	5dljB01
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	5dljB02
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	5dljC01
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	5dljC02
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	5dljD01
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	5dljD02
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	69.894 Å
Unit-cell length b length_b	193.652 Å
Unit-cell length c length_c	193.920 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	2.600 Å
Low-resolution limit resolution_low	39.835 Å
R factor r_factor	0.1808
R_work r_work	0.1794
R_free r_free	0.2075

Crystal Structure of Cas-DNA-N1 complex

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

5dlj__assembly_1__model_1

5dlj__assembly_1__model_1 | I(q)

5dlj__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of Cas-DNA-N1 complex

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

5dlj__assembly_1__model_1

5dlj__assembly_1__model_1 | I(q)

5dlj__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)