SAXSdb — 2oso

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

Hypothetical protein MJ1460

Methanocaldococcus jannaschii DSM 2661

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 CHLORIDE ION × 2 ACETATE ION × 2 GLYCEROL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1460_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–163； UniProt 1–162

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	2oso
Deposition date deposition_date	2007-02-06
Structure title title	Crystal structure of a vinyl-4-reductase family protein (mj_1460) from methanocaldococcus jannaschii dsm at 1.90 A resolution
Keywords keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, metal binding protein; METAL BINDING PROTEIN
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.

2oso__assembly_1__model_1

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

Download this curve (.dat)

2oso__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2oso__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.81 Å
Rg (electron density)	20.76 Å
Total Rg	21.61 Å
Atom count	2562
Residues	304
Excluded volume	46997 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2oso__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein MJ1460
Molecular weight formula_weight	19201.6 kDa
Mutation mutation	K132Y, K133Y, K134Y
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1420

GMAFMEKIFPDILEAIRNEEIIKESKKIPMPYFGLFALVIFDKVKELGSETSLYEIGEEFGKMLSPKNIEELKKIFKLMNFGDLEIDENKILLKNPPYKIKLSNPPYQWVSKEEPIHDFIAGILAGCLEEIFYYYFVVNEVECVSQGKDKCVFEVKEVDELNK

Source Source

Source organism organism	Methanocaldococcus jannaschii DSM 2661
NCBI taxonomy ID ncbi_taxonomy_id	243232
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2osoa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.278 — Ligand-binding domain in the NO signalling and Golgi transport
Superfamily Superfamily superfamily	d.278.1 — Ligand-binding domain in the NO signalling and Golgi transport
Family Family family	d.278.1.3 — MJ1460-like

Domain ID domain_id	d2osoa3
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

CATH v4.4 (1 domains)

Domain ID domain_id	2osoA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily	20 — Trafficking protein particle complex subunit 3

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Unit-cell length a length_a	42.100 Å
Unit-cell length b length_b	42.100 Å
Unit-cell length c length_c	172.400 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	28.736 Å
R factor r_factor	0.1920
R_work r_work	0.1890
R_free r_free	0.2450

Crystal structure of a vinyl-4-reductase family protein (mj_1460) from methanocaldococcus jannaschii dsm at 1.90 A resolution

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

Hypothetical protein MJ1460

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

2oso__assembly_1__model_1

2oso__assembly_1__model_1 | I(q)

2oso__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of a vinyl-4-reductase family protein (mj_1460) from methanocaldococcus jannaschii dsm at 1.90 A resolution

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

Hypothetical protein MJ1460

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

2oso__assembly_1__model_1

2oso__assembly_1__model_1 | I(q)

2oso__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)