SAXSdb — 2oyn

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

Hypothetical protein MJ0056

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	SODIUM ION × 2 CYTIDINE-5'-DIPHOSPHATE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y056_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–138； UniProt 2–136

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	2oyn
Deposition date deposition_date	2007-02-22
Structure title title	Crystal structure of CDP-bound protein MJ0056 from Methanococcus jannaschii, Pfam DUF120
Keywords keywords	;STRUCTURAL GENOMICS, UNKNOWN FUNCTION, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

2oyn__assembly_1__model_1

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

Download this curve (.dat)

2oyn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2oyn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.44 Å
Rg (electron density)	24.48 Å
Total Rg	24.97 Å
Atom count	2278
Residues	274
Excluded volume	41649 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2oyn__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 (4)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein MJ0056
Molecular weight formula_weight	16924.8 kDa
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	1265

MSLVKLMIIEGEVVSGLGEGRYFLSLPPYKEIFKKILGFEPYEGTLNLKLDREFDINKFKYIETEDFEFNGKRFFGVKVLPIKILIGNKKIDGAIVVPKKTYHSSEIIEIIAPMKLREQFNLKDGDVIKILIKGDKDEEGHHHHHH

Source Source

Source organism organism	Methanocaldococcus jannaschii DSM 2661
NCBI taxonomy ID ncbi_taxonomy_id	243232
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CYTIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	403.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	106

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2oyna1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.5 — Riboflavin kinase-like
Family Family family	b.43.5.2 — CTP-dependent riboflavin kinase-like

Domain ID domain_id	d2oyna2
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	2oynA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	30 — Riboflavin kinase-like

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Unit-cell length a length_a	63.480 Å
Unit-cell length b length_b	63.480 Å
Unit-cell length c length_c	73.117 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1990
R_work r_work	0.1970
R_free r_free	0.2390

Crystal structure of CDP-bound protein MJ0056 from Methanococcus jannaschii, Pfam DUF120

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

Hypothetical protein MJ0056

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

2oyn__assembly_1__model_1

2oyn__assembly_1__model_1 | I(q)

2oyn__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of CDP-bound protein MJ0056 from Methanococcus jannaschii, Pfam DUF120

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

Hypothetical protein MJ0056

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

2oyn__assembly_1__model_1

2oyn__assembly_1__model_1 | I(q)

2oyn__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)