SAXSdb — 5im6

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

Designed self-assembling icosahedral cage I32-28 trimeric subunit

Burkholderia thailandensis E264

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 120	Designed self-assembling icosahedral cage I32-28 dimeric subunit × 60 （Q9RSW5）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2SZ09_BURTA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–157； UniProt 29–183 Author chain B； PDBConstruct 3–157； UniProt 29–183 Author chain C； PDBConstruct 3–157； UniProt 29–183 Author chain D； PDBConstruct 3–157； UniProt 29–183 Author chain E； PDBConstruct 3–157； UniProt 29–183 Author chain F； PDBConstruct 3–157； UniProt 29–183 Author chain G； PDBConstruct 3–157； UniProt 29–183 Author chain H； PDBConstruct 3–157； UniProt 29–183 Author chain I； PDBConstruct 3–157； UniProt 29–183 Author chain J； PDBConstruct 3–157； UniProt 29–183 Author chain K； PDBConstruct 3–157； UniProt 29–183 Author chain L； PDBConstruct 3–157； UniProt 29–183 Author chain M； PDBConstruct 3–157； UniProt 29–183 Author chain N； PDBConstruct 3–157； UniProt 29–183 Author chain O； PDBConstruct 3–157； UniProt 29–183 Author chain P； PDBConstruct 3–157； UniProt 29–183 Author chain Q； PDBConstruct 3–157； UniProt 29–183 Author chain R； PDBConstruct 3–157； UniProt 29–183 Author chain S； PDBConstruct 3–157； UniProt 29–183 Author chain T； PDBConstruct 3–157； UniProt 29–183

Designed self-assembling icosahedral cage I32-28 dimeric subunit

Deinococcus radiodurans R1

UniProt Q9RSW5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 120	Designed self-assembling icosahedral cage I32-28 trimeric subunit × 60 （Q2SZ09）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9RSW5_DEIRA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain U； PDBConstruct 1–157； UniProt 1–157 Author chain V； PDBConstruct 1–157； UniProt 1–157 Author chain W； PDBConstruct 1–157； UniProt 1–157 Author chain X； PDBConstruct 1–157； UniProt 1–157 Author chain Y； PDBConstruct 1–157； UniProt 1–157 Author chain Z； PDBConstruct 1–157； UniProt 1–157 Author chain a； PDBConstruct 1–157； UniProt 1–157 Author chain b； PDBConstruct 1–157； UniProt 1–157 Author chain c； PDBConstruct 1–157； UniProt 1–157 Author chain d； PDBConstruct 1–157； UniProt 1–157 Author chain e； PDBConstruct 1–157； UniProt 1–157 Author chain f； PDBConstruct 1–157； UniProt 1–157 Author chain g； PDBConstruct 1–157； UniProt 1–157 Author chain h； PDBConstruct 1–157； UniProt 1–157 Author chain i； PDBConstruct 1–157； UniProt 1–157 Author chain j； PDBConstruct 1–157； UniProt 1–157 Author chain k； PDBConstruct 1–157； UniProt 1–157 Author chain l； PDBConstruct 1–157； UniProt 1–157 Author chain m； PDBConstruct 1–157； UniProt 1–157 Author chain n； PDBConstruct 1–157； UniProt 1–157

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	5im6
Deposition date deposition_date	2016-03-05
Structure title title	Crystal structure of designed two-component self-assembling icosahedral cage I32-28
Keywords keywords	;icosahedron, designed protein cage, two-component, computational design, protein engineering, Rosetta, self-assembling, co-assembling, multimerization, symmetry, nanomaterial, nanostructure, PROTEIN BINDING ;; PROTEIN BINDING
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.

5im6__assembly_1__model_1

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

Download this curve (.dat)

5im6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5im6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	121.20 Å
Total Rg	121.10 Å
Atom count	132660
Residues	18000
Excluded volume	2363400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5im6__assembly_1__model_1`	120-meric （120）	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 (2)

Entity 1 Entity 1 polymer

Description description	Designed self-assembling icosahedral cage I32-28 trimeric subunit
Molecular weight formula_weight	16798.3 kDa
Mutation mutation	D86E, A87D, A90L, D93A, G94L, A97V, V136K, A146I, R149A, R150A, R154L
Source method src_method	man
Copy count entity_count	20

Polymer Polymer

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
Atom count atom_count	44220

MGDDARIAAIGDVDELNSQIGVLLAEPLPDDVRAALSAIQHDLFDLGGELCIPGHAAITEDHLLRLALWLVHYNGQLPPLEEFILPGGARGAALAHVCRTVCRRAERSIKALGASEPLNIAPAAYVNLLSDLLFVLARVLNRAAGGADVLWDRTRAH

Source Source

Source organism organism	Burkholderia thailandensis E264
NCBI taxonomy ID ncbi_taxonomy_id	271848
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Designed self-assembling icosahedral cage I32-28 dimeric subunit
Molecular weight formula_weight	17387.7 kDa
Mutation mutation	R35Q, F36R, T54R, W122E, K129V, R137V, E140L, R141L, K144M, E148Q
Source method src_method	man
Copy count entity_count	20

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n

MILSAEQSFTLRHPHGQAAALAFVREPAAALAGVQRLRGLDSDGEQVWGELLVRVPLLGEVDLPFRSEIVRTPQGAELRPLTLTGERAWVAVSGQATAAEGGEMAFAFQFQAHLATPEAEGEGGAAFEVMVQAAAGVTLLLVAMALPQGLAAGLPPALEHHHHHH

Source Source

Source organism organism	Deinococcus radiodurans R1
NCBI taxonomy ID ncbi_taxonomy_id	243230
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	284.170 Å
Unit-cell length b length_b	284.170 Å
Unit-cell length c length_c	640.470 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	180

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	5.588 Å
Low-resolution limit resolution_low	213.200 Å
R factor r_factor	0.2274
R_work r_work	0.2259
R_free r_free	0.2403

Crystal structure of designed two-component self-assembling icosahedral cage I32-28

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

Designed self-assembling icosahedral cage I32-28 trimeric subunit

State in the Current Structure

Other States of the Same Protein in the Database

Designed self-assembling icosahedral cage I32-28 dimeric subunit

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

5im6__assembly_1__model_1

5im6__assembly_1__model_1 | I(q)

5im6__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)

Crystal structure of designed two-component self-assembling icosahedral cage I32-28

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

Designed self-assembling icosahedral cage I32-28 trimeric subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Designed self-assembling icosahedral cage I32-28 dimeric subunit

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

5im6__assembly_1__model_1

5im6__assembly_1__model_1 | I(q)

5im6__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)