SAXSdb — 2vbu

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

RIBOFLAVIN KINASE

METHANOCOCCUS JANNASCHII

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CYTIDINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 (4R)-2-METHYLPENTANE-2,4-DIOL × 3 water × 1	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 1–136； UniProt 1–136

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	2vbu
Deposition date deposition_date	2007-09-16
Structure title title	Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP
Keywords keywords	TRANSFERASE, CRADLE-LOOP BARREL, CTP-DEPENDENT KINASE, FMN; TRANSFERASE
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.

2vbu__assembly_1__model_1

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

Download this curve (.dat)

2vbu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vbu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.89 Å
Rg (electron density)	14.44 Å
Total Rg	15.77 Å
Atom count	1115
Residues	131
Excluded volume	20547 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vbu__assembly_1__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	RIBOFLAVIN KINASE
Molecular weight formula_weight	15709.5 kDa
EC 编号 ec_number	2.7.1.161
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	1283

MVKLMIIEGEVVSGLGEGRYFLSLPPYKEIFKKILGFEPYEGTLNLKLDREFDINKFKYIETEDFEFNGKRFFGVKVLPIKILIGNKKIDGAIVVPKKTYHSSEIIEIIAPMKLREQFNLKDGDVIKILIKGDKDE

Source Source

Source organism organism	METHANOCOCCUS JANNASCHII
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 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 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	(4R)-2-METHYLPENTANE-2,4-DIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	152

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2vbua_
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

CATH v4.4 (1 domains)

Domain ID domain_id	2vbuA01
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	104.845 Å
Unit-cell length b length_b	104.845 Å
Unit-cell length c length_c	32.802 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	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1630
R_work r_work	0.1610
R_free r_free	0.2120

Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP

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

RIBOFLAVIN KINASE

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

2vbu__assembly_1__model_1

2vbu__assembly_1__model_1 | I(q)

2vbu__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP

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

RIBOFLAVIN KINASE

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

2vbu__assembly_1__model_1

2vbu__assembly_1__model_1 | I(q)

2vbu__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)