6krq

Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys F80A mutant

Method: X-RAY DIFFRACTION

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

Peroxiredoxin

Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 10	CITRIC ACID × 10 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TDXH_AERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–244； UniProt 2–245 Author chain B； PDBConstruct 1–244； UniProt 2–245 Author chain C； PDBConstruct 1–244； UniProt 2–245 Author chain D； PDBConstruct 1–244； UniProt 2–245 Author chain E； PDBConstruct 1–244； UniProt 2–245 Author chain F； PDBConstruct 1–244； UniProt 2–245 Author chain G； PDBConstruct 1–244； UniProt 2–245 Author chain H； PDBConstruct 1–244； UniProt 2–245 Author chain I； PDBConstruct 1–244； UniProt 2–245 Author chain J； PDBConstruct 1–244； UniProt 2–245

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	6krq
Deposition date deposition_date	2019-08-22
Structure title title	Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys F80A mutant
Keywords keywords	Peroxiredoxin, 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.

6krq__assembly_1__model_1

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

Download this curve (.dat)

6krq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6krq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.66 Å
Rg (electron density)	50.72 Å
Total Rg	50.95 Å
Atom count	19800
Residues	2440
Excluded volume	352270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6krq__assembly_1__model_1`	decameric （10）	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	Peroxiredoxin
Molecular weight formula_weight	27840.8 kDa
EC 编号 ec_number	1.11.1.15
Mutation mutation	C50S,F80A,C207S,C213S
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	20741

PGSIPLIGERFPEMEVTTDHGVIKLPDHYVSQGKWFVLFSHPADFTPVSTTEFVSFARRYEDFQRLGVDLIGLSVDSVASHIKWKEWIERHIGVRIPFPIIADPQGTVARRLGLLHAESATHTVRGVFIVDARGVIRTMLYYPMELGRLVDEILRIVKALKLGDSLKRAVPADWPNNEIIGEGLIVPPPTTEDQARARMESGQYRSLDWWFSWDTPASRDDVEEARRYLRRAAEKPAKLLYEEA

Source Source

Source organism organism	Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
NCBI taxonomy ID ncbi_taxonomy_id	272557
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	941

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d6krqa_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d6krqb_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d6krqc_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d6krqd_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d6krqe_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d6krqf_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d6krqg_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d6krqh_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d6krqi_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d6krqj_
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.47.1.10 — Glutathione peroxidase-like

CATH v4.4 (20 domains)

Domain ID domain_id	6krqA01
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	6krqA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	6krqB01
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	6krqB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	6krqC01
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	6krqC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	6krqD01
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	6krqD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	6krqE01
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	6krqE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	6krqF01
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	6krqF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	6krqG01
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	6krqG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	6krqH01
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	6krqH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	6krqI01
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	6krqI02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	6krqJ01
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	6krqJ02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

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Unit-cell length a length_a	76.148 Å
Unit-cell length b length_b	103.156 Å
Unit-cell length c length_c	105.346 Å
Unit-cell angle α angle_alpha	106.09 °
Unit-cell angle β angle_beta	105.02 °
Unit-cell angle γ angle_gamma	92.40 °
Molecules per unit cell Z z_pdb	10

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	49.231 Å
R factor r_factor	—
R_work r_work	0.1685
R_free r_free	0.2213

Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys F80A mutant

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

Peroxiredoxin

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

6krq__assembly_1__model_1

6krq__assembly_1__model_1 | I(q)

6krq__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) 30 domains

SCOP 2.08 (10 domains)

CATH v4.4 (20 domains)

7. Citations (1)

Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys F80A mutant

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

Peroxiredoxin

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

6krq__assembly_1__model_1

6krq__assembly_1__model_1 | I(q)

6krq__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) 30 domains

SCOP 2.08 (10 domains)

CATH v4.4 (20 domains)

7. Citations (1)