SAXSdb — 4q8g

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

PAB-dependent poly(A)-specific ribonuclease subunit PAN2

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAN2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–461； UniProt 416–870 Author chain B； PDBConstruct 7–461； UniProt 416–870

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	4q8g
Deposition date deposition_date	2014-04-27
Structure title title	Structure of the Saccharomyces cerevisiae PAN2 pseudoubiquitin-hydrolase
Keywords keywords	Ubiquitin carboxyl-terminal hydrolase-like domain, UCH, PAN3, inactive, 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.

4q8g__assembly_1__model_1

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

Download this curve (.dat)

4q8g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4q8g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.36 Å
Rg (electron density)	20.75 Å
Total Rg	21.89 Å
Atom count	5363
Residues	344
Excluded volume	48449 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4q8g__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4q8g__assembly_2__model_1`	monomeric （1）	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	PAB-dependent poly(A)-specific ribonuclease subunit PAN2
Molecular weight formula_weight	53299.1 kDa
EC 编号 ec_number	3.1.13.4
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	11146

GPDSMMSQNEKLSTQEFPLLRYDRTKYGMRNAIPDYVCLRDIRKQITSGLETSDIQTYTSINKYEVPPAYSRLPLTSGRFGTDNFDFTPFNNTEYSGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDENFETTLLTDLGYLFDMMERSHGKICSSSNFQASLKSLTDKRQLENGEPQEHLEEYLESLCIRESIEDFNSSESIKRNMPQKFNRFLLSQLIKEEAQTVNHNITLNQCFGLETEIRTECSCDHYDTTVKLLPSLSISGINKTVIKQLNKKSNGQNILPYIEYAMKNVTQKNSICPTCGKTETITQECTVKNLPSVLSLELSLLDTEFSNIRSSKNWLTSEFYGSIIKNKAVLRSTASELKGTSHIFKYELNGYVAKITDNNNETRLVTYVKKYNPKENCFKWLMFNDYLVVEITEEEALKMTYPWKTPEIIIYCDAEELRKPFFSVDTYSI

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	213

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4q8gA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	4q8gB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

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Unit-cell length a length_a	68.508 Å
Unit-cell length b length_b	74.032 Å
Unit-cell length c length_c	175.081 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	8

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	48.328 Å
R factor r_factor	0.1857
R_work r_work	0.1838
R_free r_free	0.2209

Structure of the Saccharomyces cerevisiae PAN2 pseudoubiquitin-hydrolase

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

PAB-dependent poly(A)-specific ribonuclease subunit PAN2

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

4q8g__assembly_1__model_1

4q8g__assembly_1__model_1 | I(q)

4q8g__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of the Saccharomyces cerevisiae PAN2 pseudoubiquitin-hydrolase

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

PAB-dependent poly(A)-specific ribonuclease subunit PAN2

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

4q8g__assembly_1__model_1

4q8g__assembly_1__model_1 | I(q)

4q8g__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)