SAXSdb — 6yev

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

Thioredoxin 1

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Peptide methionine sulfoxide reductase MsrA × 1 （P0A744） SODIUM ION × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Peptide methionine sulfoxide reductase MsrA × 1 （P0A744） SODIUM ION × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Peptide methionine sulfoxide reductase MsrA × 1 （P0A744） SODIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THIO_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 1–109； UniProt 1–109 Author chain F； PDBConstruct 1–109； UniProt 1–109 Author chain G； PDBConstruct 1–109； UniProt 1–109

Peptide methionine sulfoxide reductase MsrA

Escherichia coli K-12

UniProt P0A744

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Thioredoxin 1 × 1 （P0AA25） SODIUM ION × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Thioredoxin 1 × 1 （P0AA25） SODIUM ION × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Thioredoxin 1 × 1 （P0AA25） SODIUM ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MSRA_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–212； UniProt 1–212 Author chain B； PDBConstruct 1–212； UniProt 1–212 Author chain C； PDBConstruct 1–212； UniProt 1–212 Author chain D； PDBConstruct 1–212； UniProt 1–212

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	6yev
Deposition date deposition_date	2020-03-25
Structure title title	Crystal structure of MsrA C206 and Trx C35S complex from Escherichia coli
Keywords keywords	Reductase, S-Methionine sulfoxide reductase, Oxidative stress, OXIDOREDUCTASE, complex, thioredoxin; 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.

6yev__assembly_1__model_1

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

Download this curve (.dat)

6yev__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6yev__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.58 Å
Rg (electron density)	21.85 Å
Total Rg	22.68 Å
Atom count	2401
Residues	312
Excluded volume	42440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6yev__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6yev__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6yev__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6yev__assembly_4__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	Thioredoxin 1
Molecular weight formula_weight	11802.5 kDa
Mutation mutation	Cys35Ser
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G
Atom count atom_count	8822

MSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPSKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Peptide methionine sulfoxide reductase MsrA
Molecular weight formula_weight	23239.8 kDa
EC 编号 ec_number	1.8.4.11
Mutation mutation	Cys51Ala, Cys86Ala, Cys198Ala
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D

MSLFDKKHLVSPADALPGRNTPMPVATLHAVNGHSMTNVPDGMEIAIFAMGAFWGVERLFWQLPGVYSTAAGYTGGYTPNPTYREVASGDTGHAEAVRIVYDPSVISYEQLLQVFWENHDPAQGMRQGNDHGTQYRSAIYPLTPEQDAAARASLERFQAAMLAADDDRHITTEIANATPFYYAEDDHQQYLHKNPYGYAGIGGIGVCLPPEA

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d6yeva_
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.58.28.1 — Peptide methionine sulfoxide reductase

Domain ID domain_id	d6yevb_
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.58.28.1 — Peptide methionine sulfoxide reductase

Domain ID domain_id	d6yevc_
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.58.28.1 — Peptide methionine sulfoxide reductase

Domain ID domain_id	d6yevd_
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.58.28.1 — Peptide methionine sulfoxide reductase

Domain ID domain_id	d6yeve_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.1 — Thioltransferase

Domain ID domain_id	d6yevf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.1 — Thioltransferase

Domain ID domain_id	d6yevg_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.1 — Thioltransferase

CATH v4.4 (3 domains)

Domain ID domain_id	6yevE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	6yevF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	6yevG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

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Unit-cell length a length_a	139.910 Å
Unit-cell length b length_b	139.910 Å
Unit-cell length c length_c	218.050 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	24

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.940 Å
Low-resolution limit resolution_low	49.710 Å
R factor r_factor	0.2302
R_work r_work	0.2288
R_free r_free	0.2576

Crystal structure of MsrA C206 and Trx C35S complex from Escherichia coli

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

Thioredoxin 1

State in the Current Structure

Other States of the Same Protein in the Database

Peptide methionine sulfoxide reductase MsrA

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

6yev__assembly_1__model_1

6yev__assembly_1__model_1 | I(q)

6yev__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (7 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of MsrA C206 and Trx C35S complex from Escherichia coli

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

Thioredoxin 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Peptide methionine sulfoxide reductase MsrA

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

6yev__assembly_1__model_1

6yev__assembly_1__model_1 | I(q)

6yev__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (7 domains)

CATH v4.4 (3 domains)

7. Citations (1)