2xpd

Reduced Thiol peroxidase (Tpx) from yersinia Pseudotuberculosis

Method: X-RAY DIFFRACTION

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

THIOL PEROXIDASE

YERSINIA PSEUDOTUBERCULOSIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q66A71_YERPS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 34–200； UniProt 1–167 Author chain B； PDBConstruct 34–200； UniProt 1–167 Author chain C； PDBConstruct 34–200； UniProt 1–167 Author chain D； PDBConstruct 34–200； UniProt 1–167 Author chain E； PDBConstruct 34–200； UniProt 1–167 Author chain F； PDBConstruct 34–200； UniProt 1–167

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	2xpd
Deposition date deposition_date	2010-08-26
Structure title title	Reduced Thiol peroxidase (Tpx) from yersinia Pseudotuberculosis
Keywords keywords	OXIDOREDUCTASE, PEROXIREDOXIN, THIOREDOXIN-FOLD, ROS PROTECTION; 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.

2xpd__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2xpd__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2xpd__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.78 Å
Rg (electron density)	20.79 Å
Total Rg	21.54 Å
Atom count	2408
Residues	332
Excluded volume	42981 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2xpd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2xpd__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2xpd__assembly_3__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	THIOL PEROXIDASE
Molecular weight formula_weight	21397.3 kDa
EC 编号 ec_number	1.11.1.15
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	7868

MHHHHHHGKPIPNPLLGLDSTENLYFQGIDPFTMTQTVHFQGNPVSVAGKLPQIGDKAKDFTLVAKDLSDVALSSFAGKRKVLNIFPSIDTGVCAASVRKFNQLAGELENTVVLCISSDLPFAQSRFCGAEGLSNVITLSTLRGADFKQAYGVAITEGPLAGLTARAVVVLDGQDNVIYSELVNEITTEPNYDAALAALK

Source Source

Source organism organism	YERSINIA PSEUDOTUBERCULOSIS
NCBI taxonomy ID ncbi_taxonomy_id	502800
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
Molecular weight formula_weight	154.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	498

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d2xpda_
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.47.1.0 — automated matches

Domain ID domain_id	d2xpdb_
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.47.1.0 — automated matches

Domain ID domain_id	d2xpdc1
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.47.1.0 — automated matches

Domain ID domain_id	d2xpdc2
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	d2xpdd_
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.47.1.0 — automated matches

Domain ID domain_id	d2xpde_
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.47.1.0 — automated matches

Domain ID domain_id	d2xpdf_
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.47.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	2xpdA00
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	2xpdB00
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	2xpdC00
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	2xpdD00
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	2xpdE00
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	2xpdF00
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	64.865 Å
Unit-cell length b length_b	92.068 Å
Unit-cell length c length_c	85.605 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	44.668 Å
R factor r_factor	0.2250
R_work r_work	0.2222
R_free r_free	0.2683

Reduced Thiol peroxidase (Tpx) from yersinia Pseudotuberculosis

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

THIOL PEROXIDASE

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

2xpd__assembly_2__model_1

2xpd__assembly_2__model_1 | I(q)

2xpd__assembly_2__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) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. Citations (2)

Reduced Thiol peroxidase (Tpx) from yersinia Pseudotuberculosis

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

THIOL PEROXIDASE

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

2xpd__assembly_2__model_1

2xpd__assembly_2__model_1 | I(q)

2xpd__assembly_2__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) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. Citations (2)