5a8a

Crystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium ammoniagenes in complex with FMN and ADP (P3 2 21)

Method: X-RAY DIFFRACTION

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

RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF

CORYNEBACTERIUM AMMONIAGENES

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FLAVIN MONONUCLEOTIDE × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 ZINC ION × 1 GLYCEROL × 1 SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FLAVIN MONONUCLEOTIDE × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 ZINC ION × 1 SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIBF_CORAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–156； UniProt 183–338 Author chain B； PDBConstruct 1–156； UniProt 183–338

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	5a8a
Deposition date deposition_date	2015-07-13
Structure title title	Crystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium ammoniagenes in complex with FMN and ADP (P3 2 21)
Keywords keywords	TRANSFERASE, RIBOFLAVIN KINASE DOMAIN, ATP-BINDING, NUCLEOTIDE-BINDING; 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.

5a8a__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5a8a__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5a8a__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	16.05 Å
Rg (electron density)	14.83 Å
Total Rg	15.96 Å
Atom count	1243
Residues	152
Excluded volume	21761 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5a8a__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5a8a__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Description description	RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
Molecular weight formula_weight	17135.1 kDa
EC 编号 ec_number	2.7.1.26
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2877

LGRHFYVTGPVVRGAGRGGKELGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNMEPEVAYAAAISVGTNPTFGDEQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFDSVEQLLEVMAKDVQKTRTLLAQDVQAHKMAPETYFLQAES

Source Source

Source organism organism	CORYNEBACTERIUM AMMONIAGENES
NCBI taxonomy ID ncbi_taxonomy_id	1697
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	321

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5a8aA00
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

Domain ID domain_id	5a8aB00
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	73.590 Å
Unit-cell length b length_b	73.590 Å
Unit-cell length c length_c	149.690 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	63.810 Å
R factor r_factor	0.1747
R_work r_work	0.1726
R_free r_free	0.2027

Crystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium ammoniagenes in complex with FMN and ADP (P3 2 21)

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

RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF

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

5a8a__assembly_2__model_1

5a8a__assembly_2__model_1 | I(q)

5a8a__assembly_2__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium ammoniagenes in complex with FMN and ADP (P3 2 21)

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

RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF

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

5a8a__assembly_2__model_1

5a8a__assembly_2__model_1 | I(q)

5a8a__assembly_2__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 (8)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)