2prr

Crystal structure of alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein (YP_296737.1) from Ralstonia eutropha JMP134 at 2.15 A resolution

Method: X-RAY DIFFRACTION

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

Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein

Ralstonia eutropha

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	DI(HYDROXYETHYL)ETHER × 12 TRIETHYLENE GLYCOL × 4 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	DI(HYDROXYETHYL)ETHER × 13 TRIETHYLENE GLYCOL × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q46Y90_RALEJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–197； UniProt 1–196 Author chain B； PDBConstruct 2–197； UniProt 1–196 Author chain C； PDBConstruct 2–197； UniProt 1–196 Author chain D； PDBConstruct 2–197； UniProt 1–196 Author chain E； PDBConstruct 2–197； UniProt 1–196 Author chain F； PDBConstruct 2–197； UniProt 1–196 Author chain G； PDBConstruct 2–197； UniProt 1–196 Author chain H； PDBConstruct 2–197； UniProt 1–196 Author chain I； PDBConstruct 2–197； UniProt 1–196 Author chain J； PDBConstruct 2–197； UniProt 1–196 Author chain K； PDBConstruct 2–197； UniProt 1–196 Author chain L； PDBConstruct 2–197； UniProt 1–196

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	2prr
Deposition date deposition_date	2007-05-04
Structure title title	Crystal structure of alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein (YP_296737.1) from Ralstonia eutropha JMP134 at 2.15 A resolution
Keywords keywords	;YP_296737.1, Carboxymuconolactone decarboxylase family, Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, 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.

2prr__assembly_1__model_1

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

Download this curve (.dat)

2prr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2prr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.55 Å
Rg (electron density)	30.83 Å
Total Rg	31.37 Å
Atom count	8999
Residues	1104
Excluded volume	161210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2prr__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2prr__assembly_2__model_1`	hexameric （6）	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	Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein
Molecular weight formula_weight	22433.7 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	19292

GMTRPAHPISRYPVPELAALPDDIRQRILEVQDKAGFVPNVFLTLAHRPDEFRAFFAYHDALMLKDGGLTKGEREMIVVATSAANQCLYCVVAHGAILRIYEKKPLVADQVAVNYLKADIPPRQRAMLDFALKVCKASHEVNEADFEALREHGFTDEDAWDIAAITAFFGLSNRMANTIGMRPNDEFFLMGRVPKSK

Source Source

Source organism organism	Ralstonia eutropha
NCBI taxonomy ID ncbi_taxonomy_id	264198
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	25

Entity 3 Entity 3 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1338

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6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2prra1
Class class	a — All alpha proteins
Fold Fold fold	a.152 — AhpD-like
Superfamily Superfamily superfamily	a.152.1 — AhpD-like
Family Family family	a.152.1.3 — Atu0492-like

Domain ID domain_id	d2prrb_
Class class	a — All alpha proteins
Fold Fold fold	a.152 — AhpD-like
Superfamily Superfamily superfamily	a.152.1 — AhpD-like
Family Family family	a.152.1.3 — Atu0492-like

Domain ID domain_id	d2prrc_
Class class	a — All alpha proteins
Fold Fold fold	a.152 — AhpD-like
Superfamily Superfamily superfamily	a.152.1 — AhpD-like
Family Family family	a.152.1.3 — Atu0492-like

Domain ID domain_id	d2prrd_
Class class	a — All alpha proteins
Fold Fold fold	a.152 — AhpD-like
Superfamily Superfamily superfamily	a.152.1 — AhpD-like
Family Family family	a.152.1.3 — Atu0492-like

Domain ID domain_id	d2prre_
Class class	a — All alpha proteins
Fold Fold fold	a.152 — AhpD-like
Superfamily Superfamily superfamily	a.152.1 — AhpD-like
Family Family family	a.152.1.3 — Atu0492-like

Domain ID domain_id	d2prrf_
Class class	a — All alpha proteins
Fold Fold fold	a.152 — AhpD-like
Superfamily Superfamily superfamily	a.152.1 — AhpD-like
Family Family family	a.152.1.3 — Atu0492-like

Domain ID domain_id	d2prrg_
Class class	a — All alpha proteins
Fold Fold fold	a.152 — AhpD-like
Superfamily Superfamily superfamily	a.152.1 — AhpD-like
Family Family family	a.152.1.3 — Atu0492-like

Domain ID domain_id	d2prrh_
Class class	a — All alpha proteins
Fold Fold fold	a.152 — AhpD-like
Superfamily Superfamily superfamily	a.152.1 — AhpD-like
Family Family family	a.152.1.3 — Atu0492-like

Domain ID domain_id	d2prri_
Class class	a — All alpha proteins
Fold Fold fold	a.152 — AhpD-like
Superfamily Superfamily superfamily	a.152.1 — AhpD-like
Family Family family	a.152.1.3 — Atu0492-like

Domain ID domain_id	d2prrj_
Class class	a — All alpha proteins
Fold Fold fold	a.152 — AhpD-like
Superfamily Superfamily superfamily	a.152.1 — AhpD-like
Family Family family	a.152.1.3 — Atu0492-like

Domain ID domain_id	d2prrk_
Class class	a — All alpha proteins
Fold Fold fold	a.152 — AhpD-like
Superfamily Superfamily superfamily	a.152.1 — AhpD-like
Family Family family	a.152.1.3 — Atu0492-like

Domain ID domain_id	d2prrl_
Class class	a — All alpha proteins
Fold Fold fold	a.152 — AhpD-like
Superfamily Superfamily superfamily	a.152.1 — AhpD-like
Family Family family	a.152.1.3 — Atu0492-like

CATH v4.4 (24 domains)

Domain ID domain_id	2prrA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 — AhpD-like

Domain ID domain_id	2prrA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

Domain ID domain_id	2prrB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 — AhpD-like

Domain ID domain_id	2prrB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

Domain ID domain_id	2prrC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 — AhpD-like

Domain ID domain_id	2prrC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

Domain ID domain_id	2prrD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 — AhpD-like

Domain ID domain_id	2prrD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

Domain ID domain_id	2prrE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 — AhpD-like

Domain ID domain_id	2prrE02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

Domain ID domain_id	2prrF01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 — AhpD-like

Domain ID domain_id	2prrF02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

Domain ID domain_id	2prrG01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 — AhpD-like

Domain ID domain_id	2prrG02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

Domain ID domain_id	2prrH01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 — AhpD-like

Domain ID domain_id	2prrH02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

Domain ID domain_id	2prrI01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 — AhpD-like

Domain ID domain_id	2prrI02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

Domain ID domain_id	2prrJ01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 — AhpD-like

Domain ID domain_id	2prrJ02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

Domain ID domain_id	2prrK01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 — AhpD-like

Domain ID domain_id	2prrK02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

Domain ID domain_id	2prrL01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 — AhpD-like

Domain ID domain_id	2prrL02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

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Unit-cell length a length_a	65.105 Å
Unit-cell length b length_b	93.953 Å
Unit-cell length c length_c	120.898 Å
Unit-cell angle α angle_alpha	84.26 °
Unit-cell angle β angle_beta	81.64 °
Unit-cell angle γ angle_gamma	77.73 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	48.912 Å
R factor r_factor	0.2130
R_work r_work	0.2110
R_free r_free	0.2620

Crystal structure of alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein (YP_296737.1) from Ralstonia eutropha JMP134 at 2.15 A resolution

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

Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein

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

2prr__assembly_1__model_1

2prr__assembly_1__model_1 | I(q)

2prr__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

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein (YP_296737.1) from Ralstonia eutropha JMP134 at 2.15 A resolution

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

Alkylhydroperoxidase AhpD core: uncharacterized peroxidase-related protein

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

2prr__assembly_1__model_1

2prr__assembly_1__model_1 | I(q)

2prr__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

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

CATH v4.4 (24 domains)

7. Citations (1)