SAXSdb — 1jra

▼

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

ERV2 PROTEIN, MITOCHONDRIAL

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	FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ERV2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–117； UniProt 71–187 Author chain B； PDBConstruct 1–117； UniProt 71–187 Author chain C； PDBConstruct 1–117； UniProt 71–187 Author chain D； PDBConstruct 1–117； UniProt 71–187

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1jra
Deposition date deposition_date	2001-08-13
Structure title title	Crystal Structure of Erv2p
Keywords keywords	FAD, sulfhydryl oxidase, helical bundle, CXXC, oxidoreductase; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1jra__assembly_1__model_1

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

Download this curve (.dat)

1jra__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jra__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.05 Å
Rg (electron density)	16.77 Å
Total Rg	17.91 Å
Atom count	1842
Residues	212
Excluded volume	32398 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jra__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1jra__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ERV2 PROTEIN, MITOCHONDRIAL
Molecular weight formula_weight	13524.4 kDa
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
Atom count atom_count	3944

LMGDDKVKKEVGRASWKYFHTLLARFPDEPTPEEREKLHTFIGLYAELYPCGECSYHFVKLIEKYPVQTSSRTAAAMWGCHIHNKVNEYLKKDIYDCATILEDYDCGCSDSDGKRVS

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	288

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1jraa_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.15 — FAD-dependent thiol oxidase
Family Family family	a.24.15.1 — FAD-dependent thiol oxidase

Domain ID domain_id	d1jrab_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.15 — FAD-dependent thiol oxidase
Family Family family	a.24.15.1 — FAD-dependent thiol oxidase

Domain ID domain_id	d1jrac_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.15 — FAD-dependent thiol oxidase
Family Family family	a.24.15.1 — FAD-dependent thiol oxidase

Domain ID domain_id	d1jrad_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.15 — FAD-dependent thiol oxidase
Family Family family	a.24.15.1 — FAD-dependent thiol oxidase

CATH v4.4 (4 domains)

Domain ID domain_id	1jraA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	310 — ERV/ALR sulfhydryl oxidase domain

Domain ID domain_id	1jraB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	310 — ERV/ALR sulfhydryl oxidase domain

Domain ID domain_id	1jraC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	310 — ERV/ALR sulfhydryl oxidase domain

Domain ID domain_id	1jraD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	310 — ERV/ALR sulfhydryl oxidase domain

▶

Unit-cell length a length_a	53.630 Å
Unit-cell length b length_b	66.810 Å
Unit-cell length c length_c	60.380 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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	20.000 Å
R factor r_factor	—
R_work r_work	0.1960
R_free r_free	0.2330

Crystal Structure of Erv2p

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

ERV2 PROTEIN, MITOCHONDRIAL

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

1jra__assembly_1__model_1

1jra__assembly_1__model_1 | I(q)

1jra__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Erv2p

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

ERV2 PROTEIN, MITOCHONDRIAL

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

1jra__assembly_1__model_1

1jra__assembly_1__model_1 | I(q)

1jra__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)