4p6i

Crystal structure of the Cas1-Cas2 complex from Escherichia coli

Method: X-RAY DIFFRACTION

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

CRISPR-associated endoribonuclease Cas2

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	CRISPR-associated endonuclease Cas1 × 4 （Q46896） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAS2_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–94； UniProt 1–94 Author chain B； PDBConstruct 1–94； UniProt 1–94

CRISPR-associated endonuclease Cas1

Escherichia coli

UniProt Q46896

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	CRISPR-associated endoribonuclease Cas2 × 2 （P45956） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

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

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	4p6i
Deposition date deposition_date	2014-03-24
Structure title title	Crystal structure of the Cas1-Cas2 complex from Escherichia coli
Keywords keywords	CRISPR-associated proteins, nuclease, hydrolase; HYDROLASE
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.

4p6i__assembly_1__model_1

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

Download this curve (.dat)

4p6i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4p6i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.91 Å
Rg (electron density)	42.82 Å
Total Rg	42.94 Å
Atom count	9925
Residues	1291
Excluded volume	178470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4p6i__assembly_1__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	CRISPR-associated endoribonuclease Cas2
Molecular weight formula_weight	11553.3 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	A,B
Atom count atom_count	10450

MSMLVVVTENVPPRLRGRLAIWLLEVRAGVYVGDVSAKIREMIWEQIAGLAEEGNVVMAWATNTETGFEFQTFGLNRRTPVDLDGLRLVSFLPVGSSENLYFQ

Source Source

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

Entity 2 Entity 2 polymer

Description description	CRISPR-associated endonuclease Cas1
Molecular weight formula_weight	33235.4 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	C,D,E,F

MTWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRVSHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMFELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCISAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNPGEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPAPPEDAQPVAIPLPVSLGDAGHRSS

Source Source

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	525

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4p6ia1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.58 — CRISPR associated protein Cas2-like
Family Family family	d.58.58.1 — CRISPR associated protein Cas2-like

Domain ID domain_id	d4p6ia2
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	d4p6ib1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.58 — CRISPR associated protein Cas2-like
Family Family family	d.58.58.1 — CRISPR associated protein Cas2-like

Domain ID domain_id	d4p6ib2
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	d4p6ic_
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	d4p6id_
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	d4p6ie_
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	d4p6if_
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 (8 domains)

Domain ID domain_id	4p6iC01
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	4p6iC02
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	4p6iD01
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	4p6iD02
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	4p6iE01
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	4p6iE02
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	4p6iF01
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	4p6iF02
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	94.875 Å
Unit-cell length b length_b	125.696 Å
Unit-cell length c length_c	99.306 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.74 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	62.848 Å
R factor r_factor	0.2258
R_work r_work	0.2254
R_free r_free	0.2451

Crystal structure of the Cas1-Cas2 complex from Escherichia coli

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

CRISPR-associated endoribonuclease Cas2

State in the Current Structure

Other States of the Same Protein in the Database

CRISPR-associated endonuclease Cas1

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

4p6i__assembly_1__model_1

4p6i__assembly_1__model_1 | I(q)

4p6i__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of the Cas1-Cas2 complex from Escherichia coli

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4p6i__assembly_1__model_1

4p6i__assembly_1__model_1 | I(q)

4p6i__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)