SAXSdb — 2xli

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

CSY4 ENDORIBONUCLEASE

PSEUDOMONAS AERUGINOSA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	5'-R(CPUPGPCPCPGPUPAPUPAPGPGPCPADGC)-3' × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A3KUJ4_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–191； UniProt 1–187

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	2xli
Deposition date deposition_date	2010-07-20
Structure title title	Crystal structure of the Csy4-crRNA complex, monoclinic form
Keywords keywords	HYDROLASE-RNA COMPLEX, ENDORIBONUCLEASE, CRISPR; HYDROLASE/RNA
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.

2xli__assembly_1__model_1

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

Download this curve (.dat)

2xli__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2xli__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.06 Å
Rg (electron density)	17.82 Å
Total Rg	18.71 Å
Atom count	1632
Residues	183
Excluded volume	27736 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2xli__assembly_1__model_1`	dimeric （2）	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	CSY4 ENDORIBONUCLEASE
Molecular weight formula_weight	21849.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1665

GSFTMDHYLDIRLRPDPEFPPAQLMSVLFGKLHQALVAQGGDRIGVSFPDLDESRSRLGERLRIHASADDLRALLARPWLEGLRDHLQFGEPAVVPHPTPYRQVSRVQAKSNPERLRRRLMRRHDLSEEEARKRIPDTVARTLDLPFVTLRSQSTGQHFRLFIRHGPLQVTAEEGGFTCYGLSKGGFVPWF

Source Source

Source organism organism	PSEUDOMONAS AERUGINOSA
NCBI taxonomy ID ncbi_taxonomy_id	208963
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	5'-R(CPUPGPCPCPGPUPAPUPAPGPGPCPADGC)-3'
Molecular weight formula_weight	5097.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

CUGCCGUAUAGGCAGC

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2xlia1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.53 — Ferredoxin-like domains from CRISPR-associated proteins
Family Family family	d.58.53.6 — CRISPR-associated protein Csy4-like

Domain ID domain_id	d2xlia2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.53 — Ferredoxin-like domains from CRISPR-associated proteins
Family Family family	d.58.53.6 — CRISPR-associated protein Csy4-like

Domain ID domain_id	d2xlia3
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

CATH v4.4 (2 domains)

Domain ID domain_id	2xliA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2540 — CRISPR-associated endoribonuclease Cas6/Csy4

Domain ID domain_id	2xliA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1960 —

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Unit-cell length a length_a	62.370 Å
Unit-cell length b length_b	46.770 Å
Unit-cell length c length_c	86.820 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.330 Å
Low-resolution limit resolution_low	19.681 Å
R factor r_factor	0.2198
R_work r_work	0.2184
R_free r_free	0.2469

Crystal structure of the Csy4-crRNA complex, monoclinic form

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

CSY4 ENDORIBONUCLEASE

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

2xli__assembly_1__model_1

2xli__assembly_1__model_1 | I(q)

2xli__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

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the Csy4-crRNA complex, monoclinic form

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

CSY4 ENDORIBONUCLEASE

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

2xli__assembly_1__model_1

2xli__assembly_1__model_1 | I(q)

2xli__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

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)