SAXSdb — 3a3g

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

Lumazine protein

Photobacterium kishitanii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C4TPG1_9GAMM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–184； UniProt 1–177 Author chain B； PDBConstruct 8–184； UniProt 1–177

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	3a3g
Deposition date deposition_date	2009-06-12
Structure title title	Crystal structure of LumP complexed with 6,7-dimethyl-8-(1'-D-ribityl) lumazine
Keywords keywords	luminous bacteria, lumazine protein, photobacterium, LUMINESCENT PROTEIN; LUMINESCENT 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.

3a3g__assembly_1__model_1

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

Download this curve (.dat)

3a3g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3a3g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.17 Å
Rg (electron density)	16.00 Å
Total Rg	17.08 Å
Atom count	1406
Residues	180
Excluded volume	25156 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3a3g__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3a3g__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 (3)

Entity 1 Entity 1 polymer

Description description	Lumazine protein
Molecular weight formula_weight	20911.6 kDa
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	2983

MFKGIVQGAGIIKKISKNDDTQRHGITFPKDILESVEKGTVMLVNGCSLTVVRISGDVVYFDIDQAINTTTFRELEVGNKVNLEVRPEFGSLLGKGALTGNIKGVATVDNITEEEDRLKVYIKIPKDLIENILSEDHIGINGVSHSIEEISDDIIFINYPKNLSITTNLGTLEKGSDVNVETLNVSNEWD

Source Source

Source organism organism	Photobacterium kishitanii
NCBI taxonomy ID ncbi_taxonomy_id	318456
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol
Molecular weight formula_weight	326.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	184

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3a3gA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3a3gA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3a3gB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3a3gB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	46.689 Å
Unit-cell length b length_b	46.584 Å
Unit-cell length c length_c	161.587 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	44.766 Å
R factor r_factor	0.1977
R_work r_work	0.1947
R_free r_free	0.2548

Crystal structure of LumP complexed with 6,7-dimethyl-8-(1'-D-ribityl) lumazine

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

Lumazine protein

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

3a3g__assembly_1__model_1

3a3g__assembly_1__model_1 | I(q)

3a3g__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of LumP complexed with 6,7-dimethyl-8-(1'-D-ribityl) lumazine

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

Lumazine protein

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

3a3g__assembly_1__model_1

3a3g__assembly_1__model_1 | I(q)

3a3g__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)