SAXSdb — 9g3i

▼

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 100	No other associated polymer	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 A； PDBConstruct 2–36； UniProt 120–154 Author chain A； PDBConstruct 47–163； UniProt 3–119 Author chain AA； PDBConstruct 2–36； UniProt 120–154 Author chain AA； PDBConstruct 47–163； UniProt 3–119 Author chain AB； PDBConstruct 2–36； UniProt 120–154 Author chain AB； PDBConstruct 47–163； UniProt 3–119 Author chain AC； PDBConstruct 2–36； UniProt 120–154 Author chain AC； PDBConstruct 47–163； UniProt 3–119 Author chain B； PDBConstruct 2–36； UniProt 120–154 Author chain B； PDBConstruct 47–163； UniProt 3–119 Author chain BA； PDBConstruct 2–36； UniProt 120–154 Author chain BA； PDBConstruct 47–163； UniProt 3–119 Author chain BB； PDBConstruct 2–36； UniProt 120–154 Author chain BB； PDBConstruct 47–163； UniProt 3–119 Author chain BC； PDBConstruct 2–36； UniProt 120–154 Author chain BC； PDBConstruct 47–163； UniProt 3–119 Author chain C； PDBConstruct 2–36； UniProt 120–154 Author chain C； PDBConstruct 47–163； UniProt 3–119 Author chain CA； PDBConstruct 2–36； UniProt 120–154 Author chain CA； PDBConstruct 47–163； UniProt 3–119 Author chain CB； PDBConstruct 2–36； UniProt 120–154 Author chain CB； PDBConstruct 47–163； UniProt 3–119 Author chain CC； PDBConstruct 2–36； UniProt 120–154 Author chain CC； PDBConstruct 47–163； UniProt 3–119 Author chain D； PDBConstruct 2–36； UniProt 120–154 Author chain D； PDBConstruct 47–163； UniProt 3–119 Author chain DA； PDBConstruct 2–36； UniProt 120–154 Author chain DA； PDBConstruct 47–163； UniProt 3–119 Author chain DB； PDBConstruct 2–36； UniProt 120–154 Author chain DB； PDBConstruct 47–163； UniProt 3–119 Author chain DC； PDBConstruct 2–36； UniProt 120–154 Author chain DC； PDBConstruct 47–163； UniProt 3–119 Author chain E； PDBConstruct 2–36； UniProt 120–154 Author chain E； PDBConstruct 47–163； UniProt 3–119 Author chain EA； PDBConstruct 2–36； UniProt 120–154 Author chain EA； PDBConstruct 47–163； UniProt 3–119 Author chain EB； PDBConstruct 2–36； UniProt 120–154 Author chain EB； PDBConstruct 47–163； UniProt 3–119 Author chain EC； PDBConstruct 2–36； UniProt 120–154 Author chain EC； PDBConstruct 47–163； UniProt 3–119 Author chain F； PDBConstruct 2–36； UniProt 120–154 Author chain F； PDBConstruct 47–163； UniProt 3–119 Author chain FA； PDBConstruct 2–36； UniProt 120–154 Author chain FA； PDBConstruct 47–163； UniProt 3–119 Author chain FB； PDBConstruct 2–36； UniProt 120–154 Author chain FB； PDBConstruct 47–163； UniProt 3–119 Author chain FC； PDBConstruct 2–36； UniProt 120–154 Author chain FC； PDBConstruct 47–163； UniProt 3–119 Author chain G； PDBConstruct 2–36； UniProt 120–154 Author chain G； PDBConstruct 47–163； UniProt 3–119 Author chain GA； PDBConstruct 2–36； UniProt 120–154 Author chain GA； PDBConstruct 47–163； UniProt 3–119 Author chain GB； PDBConstruct 2–36； UniProt 120–154 Author chain GB； PDBConstruct 47–163； UniProt 3–119 Author chain GC； PDBConstruct 2–36； UniProt 120–154 Author chain GC； PDBConstruct 47–163； UniProt 3–119 Author chain H； PDBConstruct 2–36； UniProt 120–154 Author chain H； PDBConstruct 47–163； UniProt 3–119 Author chain HA； PDBConstruct 2–36； UniProt 120–154 Author chain HA； PDBConstruct 47–163； UniProt 3–119 Author chain HB； PDBConstruct 2–36； UniProt 120–154 Author chain HB； PDBConstruct 47–163； UniProt 3–119 Author chain HC； PDBConstruct 2–36； UniProt 120–154 Author chain HC； PDBConstruct 47–163； UniProt 3–119 Author chain I； PDBConstruct 2–36； UniProt 120–154 Author chain I； PDBConstruct 47–163； UniProt 3–119 Author chain IA； PDBConstruct 2–36； UniProt 120–154 Author chain IA； PDBConstruct 47–163； UniProt 3–119 Author chain IB； PDBConstruct 2–36； UniProt 120–154 Author chain IB； PDBConstruct 47–163； UniProt 3–119 Author chain IC； PDBConstruct 2–36； UniProt 120–154 Author chain IC； PDBConstruct 47–163； UniProt 3–119 Author chain J； PDBConstruct 2–36； UniProt 120–154 Author chain J； PDBConstruct 47–163； UniProt 3–119 Author chain JA； PDBConstruct 2–36； UniProt 120–154 Author chain JA； PDBConstruct 47–163； UniProt 3–119 Author chain JB； PDBConstruct 2–36； UniProt 120–154 Author chain JB； PDBConstruct 47–163； UniProt 3–119 Author chain JC； PDBConstruct 2–36； UniProt 120–154 Author chain JC； PDBConstruct 47–163； UniProt 3–119 Author chain K； PDBConstruct 2–36； UniProt 120–154 Author chain K； PDBConstruct 47–163； UniProt 3–119 Author chain KA； PDBConstruct 2–36； UniProt 120–154 Author chain KA； PDBConstruct 47–163； UniProt 3–119 Author chain KB； PDBConstruct 2–36； UniProt 120–154 Author chain KB； PDBConstruct 47–163； UniProt 3–119 Author chain KC； PDBConstruct 2–36； UniProt 120–154 Author chain KC； PDBConstruct 47–163； UniProt 3–119 Author chain L； PDBConstruct 2–36； UniProt 120–154 Author chain L； PDBConstruct 47–163； UniProt 3–119 Author chain LA； PDBConstruct 2–36； UniProt 120–154 Author chain LA； PDBConstruct 47–163； UniProt 3–119 Author chain LB； PDBConstruct 2–36； UniProt 120–154 Author chain LB； PDBConstruct 47–163； UniProt 3–119 Author chain LC； PDBConstruct 2–36； UniProt 120–154 Author chain LC； PDBConstruct 47–163； UniProt 3–119 Author chain M； PDBConstruct 2–36； UniProt 120–154 Author chain M； PDBConstruct 47–163； UniProt 3–119 Author chain MA； PDBConstruct 2–36； UniProt 120–154 Author chain MA； PDBConstruct 47–163； UniProt 3–119 Author chain MB； PDBConstruct 2–36； UniProt 120–154 Author chain MB； PDBConstruct 47–163； UniProt 3–119 Author chain MC； PDBConstruct 2–36； UniProt 120–154 Author chain MC； PDBConstruct 47–163； UniProt 3–119 Author chain N； PDBConstruct 2–36； UniProt 120–154 Author chain N； PDBConstruct 47–163； UniProt 3–119 Author chain NA； PDBConstruct 2–36； UniProt 120–154 Author chain NA； PDBConstruct 47–163； UniProt 3–119 Author chain NB； PDBConstruct 2–36； UniProt 120–154 Author chain NB； PDBConstruct 47–163； UniProt 3–119 Author chain NC； PDBConstruct 2–36； UniProt 120–154 Author chain NC； PDBConstruct 47–163； UniProt 3–119 Author chain O； PDBConstruct 2–36； UniProt 120–154 Author chain O； PDBConstruct 47–163； UniProt 3–119 Author chain OA； PDBConstruct 2–36； UniProt 120–154 Author chain OA； PDBConstruct 47–163； UniProt 3–119 Author chain OB； PDBConstruct 2–36； UniProt 120–154 Author chain OB； PDBConstruct 47–163； UniProt 3–119 Author chain OC； PDBConstruct 2–36； UniProt 120–154 Author chain OC； PDBConstruct 47–163； UniProt 3–119 Author chain P； PDBConstruct 2–36； UniProt 120–154 Author chain P； PDBConstruct 47–163； UniProt 3–119 Author chain PA； PDBConstruct 2–36； UniProt 120–154 Author chain PA； PDBConstruct 47–163； UniProt 3–119 Author chain PB； PDBConstruct 2–36； UniProt 120–154 Author chain PB； PDBConstruct 47–163； UniProt 3–119 Author chain PC； PDBConstruct 2–36； UniProt 120–154 Author chain PC； PDBConstruct 47–163； UniProt 3–119 Author chain Q； PDBConstruct 2–36； UniProt 120–154 Author chain Q； PDBConstruct 47–163； UniProt 3–119 Author chain QA； PDBConstruct 2–36； UniProt 120–154 Author chain QA； PDBConstruct 47–163； UniProt 3–119 Author chain QB； PDBConstruct 2–36； UniProt 120–154 Author chain QB； PDBConstruct 47–163； UniProt 3–119 Author chain QC； PDBConstruct 2–36； UniProt 120–154 Author chain QC； PDBConstruct 47–163； UniProt 3–119 Author chain R； PDBConstruct 2–36； UniProt 120–154 Author chain R； PDBConstruct 47–163； UniProt 3–119 Author chain RA； PDBConstruct 2–36； UniProt 120–154 Author chain RA； PDBConstruct 47–163； UniProt 3–119 Author chain RB； PDBConstruct 2–36； UniProt 120–154 Author chain RB； PDBConstruct 47–163； UniProt 3–119 Author chain RC； PDBConstruct 2–36； UniProt 120–154 Author chain RC； PDBConstruct 47–163； UniProt 3–119 Author chain S； PDBConstruct 2–36； UniProt 120–154 Author chain S； PDBConstruct 47–163； UniProt 3–119 Author chain SA； PDBConstruct 2–36； UniProt 120–154 Author chain SA； PDBConstruct 47–163； UniProt 3–119 Author chain SB； PDBConstruct 2–36； UniProt 120–154 Author chain SB； PDBConstruct 47–163； UniProt 3–119 Author chain SC； PDBConstruct 2–36； UniProt 120–154 Author chain SC； PDBConstruct 47–163； UniProt 3–119 Author chain T； PDBConstruct 2–36； UniProt 120–154 Author chain T； PDBConstruct 47–163； UniProt 3–119 Author chain TA； PDBConstruct 2–36； UniProt 120–154 Author chain TA； PDBConstruct 47–163； UniProt 3–119 Author chain TB； PDBConstruct 2–36； UniProt 120–154 Author chain TB； PDBConstruct 47–163； UniProt 3–119 Author chain TC； PDBConstruct 2–36； UniProt 120–154 Author chain TC； PDBConstruct 47–163； UniProt 3–119 Author chain U； PDBConstruct 2–36； UniProt 120–154 Author chain U； PDBConstruct 47–163； UniProt 3–119 Author chain UA； PDBConstruct 2–36； UniProt 120–154 Author chain UA； PDBConstruct 47–163； UniProt 3–119 Author chain UB； PDBConstruct 2–36； UniProt 120–154 Author chain UB； PDBConstruct 47–163； UniProt 3–119 Author chain UC； PDBConstruct 2–36； UniProt 120–154 Author chain UC； PDBConstruct 47–163； UniProt 3–119 Author chain V； PDBConstruct 2–36； UniProt 120–154 Author chain V； PDBConstruct 47–163； UniProt 3–119 Author chain VA； PDBConstruct 2–36； UniProt 120–154 Author chain VA； PDBConstruct 47–163； UniProt 3–119 Author chain VB； PDBConstruct 2–36； UniProt 120–154 Author chain VB； PDBConstruct 47–163； UniProt 3–119 Author chain VC； PDBConstruct 2–36； UniProt 120–154 Author chain VC； PDBConstruct 47–163； UniProt 3–119 Author chain W； PDBConstruct 2–36； UniProt 120–154 Author chain W； PDBConstruct 47–163； UniProt 3–119 Author chain WA； PDBConstruct 2–36； UniProt 120–154 Author chain WA； PDBConstruct 47–163； UniProt 3–119 Author chain WB； PDBConstruct 2–36； UniProt 120–154 Author chain WB； PDBConstruct 47–163； UniProt 3–119 Author chain X； PDBConstruct 2–36； UniProt 120–154 Author chain X； PDBConstruct 47–163； UniProt 3–119 Author chain XA； PDBConstruct 2–36； UniProt 120–154 Author chain XA； PDBConstruct 47–163； UniProt 3–119 Author chain XB； PDBConstruct 2–36； UniProt 120–154 Author chain XB； PDBConstruct 47–163； UniProt 3–119 Author chain Y； PDBConstruct 2–36； UniProt 120–154 Author chain Y； PDBConstruct 47–163； UniProt 3–119 Author chain YA； PDBConstruct 2–36； UniProt 120–154 Author chain YA； PDBConstruct 47–163； UniProt 3–119 Author chain YB； PDBConstruct 2–36； UniProt 120–154 Author chain YB； PDBConstruct 47–163； UniProt 3–119 Author chain Z； PDBConstruct 2–36； UniProt 120–154 Author chain Z； PDBConstruct 47–163； UniProt 3–119 Author chain ZA； PDBConstruct 2–36； UniProt 120–154 Author chain ZA； PDBConstruct 47–163； UniProt 3–119 Author chain ZB； PDBConstruct 2–36； UniProt 120–154 Author chain ZB； PDBConstruct 47–163； UniProt 3–119

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9g3i
Deposition date deposition_date	2024-07-12
Structure title title	Circularly permuted lumazine synthase twisted tube with 18 Angstrom gap between double strands
Keywords keywords	;protein cage, protein engineering, self-assembly, geometry, helical reconstruction, bionanotechnology, polymorphism, pentamer, DE NOVO PROTEIN ;; DE NOVO PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

9g3i__assembly_1__model_1

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

Download this curve (.dat)

9g3i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9g3i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	98.53 Å
Rg (electron density)	97.13 Å
Total Rg	97.22 Å
Atom count	114640
Residues	15260
Excluded volume	2044900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9g3i__assembly_1__model_1`	100-meric （100）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (1)

▶

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	2.85 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	807640

Description description	6,7-dimethyl-8-ribityllumazine synthase
Molecular weight formula_weight	17465.9 kDa
EC 编号 ec_number	2.5.1.78
Mutation mutation	119 circular permutation,C37S,A85C
Source method src_method	man
Copy count entity_count	100

Polymer type type	polypeptide(L)
Chain IDs strand_id	;A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC,IC,JC,KC,LC,MC,NC,OC,PC,QC,RC,SC,TC,UC,VC ;
Atom count atom_count	114640

Circularly permuted lumazine synthase twisted tube with 18 Angstrom gap between double strands

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

9g3i__assembly_1__model_1

9g3i__assembly_1__model_1 | I(q)

9g3i__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)

Source organism organism	Aquifex aeolicus VF5
NCBI taxonomy ID ncbi_taxonomy_id	224324
Host organism host_organism	Escherichia coli #1/H766

Circularly permuted lumazine synthase twisted tube with 18 Angstrom gap between double strands

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

9g3i__assembly_1__model_1

9g3i__assembly_1__model_1 | I(q)

9g3i__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)