SAXSdb — 4nwp

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

Putative uncharacterized protein

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Uncharacterized protein × 12 （Q9I2D8） SULFATE ION × 84 AMMONIUM ION × 3 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O58404_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–172； UniProt 1–172 Author chain B； PDBConstruct 1–172； UniProt 1–172 Author chain C； PDBConstruct 1–172； UniProt 1–172 Author chain D； PDBConstruct 1–172； UniProt 1–172

Uncharacterized protein

Pseudomonas aeruginosa

UniProt Q9I2D8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Putative uncharacterized protein × 12 （O58404） SULFATE ION × 84 AMMONIUM ION × 3 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9I2D8_PSEAE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–123； UniProt 1–123 Author chain F； PDBConstruct 1–123； UniProt 1–123 Author chain G； PDBConstruct 1–123； UniProt 1–123 Author chain H； PDBConstruct 1–123； UniProt 1–123

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	4nwp
Deposition date deposition_date	2013-12-06
Structure title title	Computationally Designed Two-Component Self-Assembling Tetrahedral Cage, T33-21, Crystallized in Space Group R32
Keywords keywords	;two-component, self-assembling, tetrahedron, designed protein cage, computational design, computational biology, protein engineering, multimerization, 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.

4nwp__assembly_1__model_1

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

Download this curve (.dat)

4nwp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4nwp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.45 Å
Rg (electron density)	44.75 Å
Total Rg	45.00 Å
Atom count	23763
Residues	3138
Excluded volume	425020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4nwp__assembly_1__model_1`	24-meric （24）	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 (5)

Entity 1 Entity 1 polymer

Description description	Putative uncharacterized protein
Molecular weight formula_weight	19316.6 kDa
Mutation mutation	K85A, E88L, G89K, S92L, E95M, E126L, A130L, L133T, K140A, L143A, V144A, N147L, R148A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8248

MRITTKVGDKGSTRLFGGEEVWKDSPIIEANGTLDELTSFIGEAKHYVDEEMKGILEEIQNDIYKIMGEIGSKGKIEGISEERIAWLLKLILRYMEMVNLKSFVLPGGTLESAKLDVCRTIARRALRKVLTVTREFGIGAEAAAYLLALSDLLFLLARVIEIEKNKLKEVRS

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Uncharacterized protein
Molecular weight formula_weight	14346.3 kDa
Mutation mutation	A27K, A74I, Q78T, A79L, E82A, E86A, G90E, A112L
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

MPHLVIEATANLRLETSPGELLEQANKALFASGQFGEADIKSRFVTLEAYRQGTAAVERAYLHACLSILDGRDIATRTLLGASLCAVLAEAVAGGGEEGVQVSVEVREMERLSYAKRVVARQRLEHHHHHH

Source Source

Source organism organism	Pseudomonas aeruginosa
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	28

Entity 4 Entity 4 non-polymer

Description description	AMMONIUM ION
Molecular weight formula_weight	18.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	225

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4nwpA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	4nwpB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	4nwpC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	4nwpD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	4nwpE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	4nwpF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	4nwpG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	4nwpH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

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Unit-cell length a length_a	113.350 Å
Unit-cell length b length_b	113.350 Å
Unit-cell length c length_c	634.880 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	72

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	93.780 Å
R factor r_factor	0.1910
R_work r_work	0.1880
R_free r_free	0.2180

Computationally Designed Two-Component Self-Assembling Tetrahedral Cage, T33-21, Crystallized in Space Group R32

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

Putative uncharacterized protein

State in the Current Structure

Other States of the Same Protein in the Database

Uncharacterized 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

4nwp__assembly_1__model_1

4nwp__assembly_1__model_1 | I(q)

4nwp__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Computationally Designed Two-Component Self-Assembling Tetrahedral Cage, T33-21, Crystallized in Space Group R32

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

Putative uncharacterized 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

Uncharacterized 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

4nwp__assembly_1__model_1

4nwp__assembly_1__model_1 | I(q)

4nwp__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)