SAXSdb — 4ogp

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

DNA topoisomerase 2-associated protein PAT1

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	2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 1,2-ETHANEDIOL × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAT1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–324； UniProt 473–796 Author chain B； PDBConstruct 1–324； UniProt 473–796

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	4ogp
Deposition date deposition_date	2014-01-16
Structure title title	Structure of C-terminal domain from S. cerevisiae Pat1 decapping activator (Space group : P21)
Keywords keywords	ARM-repeat fold, Dcp2, Lsm1-7, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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.

4ogp__assembly_1__model_1

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

Download this curve (.dat)

4ogp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ogp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.16 Å
Rg (electron density)	22.78 Å
Total Rg	23.67 Å
Atom count	2594
Residues	314
Excluded volume	47154 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ogp__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ogp__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 (4)

Entity 1 Entity 1 polymer

Description description	DNA topoisomerase 2-associated protein PAT1
Molecular weight formula_weight	38484.4 kDa
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	5361

GGKKFILELIETVYEEILDLEANLRNGQQTDSTAMWEALHIDDSSYDVNPFISMLSFDKGIKIMPRIFNFLDKQQKLKILQKIFNELSHLQIIILSSYKTTPKPTLTQLKKVDLFQMIILKIIVSFLSNNSNFIEIMGLLLQLIRNNNVSFLTTSKIGLNLITILISRAALIKQDSSRSNILSSPEISTWNEIYDKLFTSLESKIQLIFPPREYNDHIMRLQNDKFMDEAYIWQFLASLALSGKLNHQRIIIDEVRDEIFATINEAETLQKKEKELSVLPQRSQELDTELKSIIYNKEKLYQDLNLFLNVMGLVYRDGEISELKHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	141

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Unit-cell length a length_a	55.120 Å
Unit-cell length b length_b	88.460 Å
Unit-cell length c length_c	67.910 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.08 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	46.591 Å
R factor r_factor	0.2068
R_work r_work	0.2040
R_free r_free	0.2606

Structure of C-terminal domain from S. cerevisiae Pat1 decapping activator (Space group : P21)

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

DNA topoisomerase 2-associated protein PAT1

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

4ogp__assembly_1__model_1

4ogp__assembly_1__model_1 | I(q)

4ogp__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Structure of C-terminal domain from S. cerevisiae Pat1 decapping activator (Space group : P21)

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

DNA topoisomerase 2-associated protein PAT1

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

4ogp__assembly_1__model_1

4ogp__assembly_1__model_1 | I(q)

4ogp__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)