SAXSdb — 3pim

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

Peptide methionine sulfoxide reductase

Saccharomyces cerevisiae

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MSRA_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–187； UniProt 2–184 Author chain B； PDBConstruct 5–187； UniProt 2–184 Author chain C； PDBConstruct 5–187； UniProt 2–184

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	3pim
Deposition date deposition_date	2010-11-07
Structure title title	Crystal structure of Mxr1 from Saccharomyces cerevisiae in unusual oxidized form
Keywords keywords	methionine-S-sulfoxide reductase, Oxidoreductase; OXIDOREDUCTASE
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.

3pim__assembly_1__model_1

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

Download this curve (.dat)

3pim__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pim__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.47 Å
Rg (electron density)	20.63 Å
Total Rg	21.57 Å
Atom count	2857
Residues	350
Excluded volume	50508 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pim__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pim__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 (2)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3pima1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.28 — Peptide methionine sulfoxide reductase
Family Family family	d.58.28.0 — automated matches

Domain ID domain_id	d3pima2
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	d3pimb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.28 — Peptide methionine sulfoxide reductase
Family Family family	d.58.28.0 — automated matches

Domain ID domain_id	d3pimb2
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	d3pimc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.28 — Peptide methionine sulfoxide reductase
Family Family family	d.58.28.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	3pimA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1060 — Peptide Methionine Sulfoxide Reductase; Chain A
Homologous superfamily homologous superfamily	10 — Peptide methionine sulphoxide reductase MsrA

Domain ID domain_id	3pimB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1060 — Peptide Methionine Sulfoxide Reductase; Chain A
Homologous superfamily homologous superfamily	10 — Peptide methionine sulphoxide reductase MsrA

Domain ID domain_id	3pimC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1060 — Peptide Methionine Sulfoxide Reductase; Chain A
Homologous superfamily homologous superfamily	10 — Peptide methionine sulphoxide reductase MsrA

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Unit-cell length a length_a	111.894 Å
Unit-cell length b length_b	111.894 Å
Unit-cell length c length_c	108.124 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2375
R_work r_work	0.2361
R_free r_free	0.2645

Description description	Peptide methionine sulfoxide reductase
Molecular weight formula_weight	21511.2 kDa
EC 编号 ec_number	1.8.4.11
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4421

Crystal structure of Mxr1 from Saccharomyces cerevisiae in unusual oxidized form

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

Peptide methionine sulfoxide reductase

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

3pim__assembly_1__model_1

3pim__assembly_1__model_1 | I(q)

3pim__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

7. Citations (1)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	234

Crystal structure of Mxr1 from Saccharomyces cerevisiae in unusual oxidized form

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

Peptide methionine sulfoxide reductase

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

3pim__assembly_1__model_1

3pim__assembly_1__model_1 | I(q)

3pim__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

7. Citations (1)