SAXSdb — 9ryu

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

6,7-dimethyl-8-ribityllumazine synthase

Aquifex aeolicus VF5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 60	PHOSPHATE ION × 60 water × 60	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RISB_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A1； PDBConstruct 1–154； UniProt 1–154 Author chain A2； PDBConstruct 1–154； UniProt 1–154 Author chain A3； PDBConstruct 1–154； UniProt 1–154 Author chain A4； PDBConstruct 1–154； UniProt 1–154 Author chain A5； PDBConstruct 1–154； UniProt 1–154 Author chain B1； PDBConstruct 1–154； UniProt 1–154 Author chain B2； PDBConstruct 1–154； UniProt 1–154 Author chain B3； PDBConstruct 1–154； UniProt 1–154 Author chain B4； PDBConstruct 1–154； UniProt 1–154 Author chain B5； PDBConstruct 1–154； UniProt 1–154 Author chain C1； PDBConstruct 1–154； UniProt 1–154 Author chain C2； PDBConstruct 1–154； UniProt 1–154 Author chain C3； PDBConstruct 1–154； UniProt 1–154 Author chain C4； PDBConstruct 1–154； UniProt 1–154 Author chain C5； PDBConstruct 1–154； UniProt 1–154 Author chain D1； PDBConstruct 1–154； UniProt 1–154 Author chain D2； PDBConstruct 1–154； UniProt 1–154 Author chain D3； PDBConstruct 1–154； UniProt 1–154 Author chain D4； PDBConstruct 1–154； UniProt 1–154 Author chain D5； PDBConstruct 1–154； UniProt 1–154 Author chain E1； PDBConstruct 1–154； UniProt 1–154 Author chain E2； PDBConstruct 1–154； UniProt 1–154 Author chain E3； PDBConstruct 1–154； UniProt 1–154 Author chain E4； PDBConstruct 1–154； UniProt 1–154 Author chain E5； PDBConstruct 1–154； UniProt 1–154 Author chain F1； PDBConstruct 1–154； UniProt 1–154 Author chain F2； PDBConstruct 1–154； UniProt 1–154 Author chain F3； PDBConstruct 1–154； UniProt 1–154 Author chain F4； PDBConstruct 1–154； UniProt 1–154 Author chain F5； PDBConstruct 1–154； UniProt 1–154 Author chain G1； PDBConstruct 1–154； UniProt 1–154 Author chain G2； PDBConstruct 1–154； UniProt 1–154 Author chain G3； PDBConstruct 1–154； UniProt 1–154 Author chain G4； PDBConstruct 1–154； UniProt 1–154 Author chain G5； PDBConstruct 1–154； UniProt 1–154 Author chain H1； PDBConstruct 1–154； UniProt 1–154 Author chain H2； PDBConstruct 1–154； UniProt 1–154 Author chain H3； PDBConstruct 1–154； UniProt 1–154 Author chain H4； PDBConstruct 1–154； UniProt 1–154 Author chain H5； PDBConstruct 1–154； UniProt 1–154 Author chain I1； PDBConstruct 1–154； UniProt 1–154 Author chain I2； PDBConstruct 1–154； UniProt 1–154 Author chain I3； PDBConstruct 1–154； UniProt 1–154 Author chain I4； PDBConstruct 1–154； UniProt 1–154 Author chain I5； PDBConstruct 1–154； UniProt 1–154 Author chain J1； PDBConstruct 1–154； UniProt 1–154 Author chain J2； PDBConstruct 1–154； UniProt 1–154 Author chain J3； PDBConstruct 1–154； UniProt 1–154 Author chain J4； PDBConstruct 1–154； UniProt 1–154 Author chain J5； PDBConstruct 1–154； UniProt 1–154 Author chain K1； PDBConstruct 1–154； UniProt 1–154 Author chain K2； PDBConstruct 1–154； UniProt 1–154 Author chain K3； PDBConstruct 1–154； UniProt 1–154 Author chain K4； PDBConstruct 1–154； UniProt 1–154 Author chain K5； PDBConstruct 1–154； UniProt 1–154 Author chain L1； PDBConstruct 1–154； UniProt 1–154 Author chain L2； PDBConstruct 1–154； UniProt 1–154 Author chain L3； PDBConstruct 1–154； UniProt 1–154 Author chain L4； PDBConstruct 1–154； UniProt 1–154 Author chain L5； PDBConstruct 1–154； UniProt 1–154

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	9ryu
Deposition date deposition_date	2025-07-15
Structure title title	Aquifex aeolicus lumazine synthase L121A mutant 12-pentamer cage
Keywords keywords	protein cage, protein engineering, self-assembly, geometry, pentamer, encapsulation, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

9ryu__assembly_1__model_1

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

Download this curve (.dat)

9ryu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ryu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	66.05 Å
Rg (electron density)	64.95 Å
Total Rg	65.23 Å
Atom count	70680
Residues	9240
Excluded volume	1259400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ryu__assembly_1__model_1`	60-meric （60）	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	6,7-dimethyl-8-ribityllumazine synthase
Molecular weight formula_weight	18084.6 kDa
EC 编号 ec_number	2.5.1.78
Source method src_method	man
Copy count entity_count	60

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	;A1,A2,A3,A4,A5,B1,B2,B3,B4,B5,C1,C2,C3,C4,C5,D1,D2,D3,D4,D5,E1,E2,E3,E4,E5,F1,F2,F3,F4,F5,G1,G2,G3,G4,G5,H1,H2,H3,H4,H5,I1,I2,I3,I4,I5,J1,J2,J3,J4,J5,K1,K2,K3,K4,K5,L1,L2,L3,L4,L5 ;
Atom count atom_count	72870

MEIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEIPVAAGELARKEDIDAVIAIGVLIRGATPHFDYIASEVSKGLANLSLELRKPITFGVITADTAEQAIERAGTKHGNKGWEAALSAIEMANLFKSLRLEGGWSHPQFEK

Source Source

Source organism organism	Aquifex aeolicus VF5
NCBI taxonomy ID ncbi_taxonomy_id	224324
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	60

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2190

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	1.71 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1507746

Aquifex aeolicus lumazine synthase L121A mutant 12-pentamer cage

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

6,7-dimethyl-8-ribityllumazine synthase

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

9ryu__assembly_1__model_1

9ryu__assembly_1__model_1 | I(q)

9ryu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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

7. Citations (1)

Aquifex aeolicus lumazine synthase L121A mutant 12-pentamer cage

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

6,7-dimethyl-8-ribityllumazine synthase

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

9ryu__assembly_1__model_1

9ryu__assembly_1__model_1 | I(q)

9ryu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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

7. Citations (1)