SAXSdb — 1tx9

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

Scaffolding protein D

Enterobacteria phage phiX174

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VGD_BPPHX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–151； UniProt 1–151 Author chain B； PDBConstruct 1–151； UniProt 1–151

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	1tx9
Deposition date deposition_date	2004-06-24
Structure title title	gpd prior to capsid assembly
Keywords keywords	scaffolding protein, phiX174, assembly, conformational switching, STRUCTURAL PROTEIN; STRUCTURAL 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.

1tx9__assembly_1__model_1

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

Download this curve (.dat)

1tx9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1tx9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.90 Å
Rg (electron density)	18.82 Å
Total Rg	19.74 Å
Atom count	2125
Residues	271
Excluded volume	37961 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1tx9__assembly_1__model_1`	dimeric （2）	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 (1)

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1tx9a1
Class class	a — All alpha proteins
Fold Fold fold	a.84 — Scaffolding protein gpD of bacteriophage procapsid
Superfamily Superfamily superfamily	a.84.1 — Scaffolding protein gpD of bacteriophage procapsid
Family Family family	a.84.1.1 — Scaffolding protein gpD of bacteriophage procapsid

CATH v4.4 (2 domains)

Domain ID domain_id	1tx9A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1850 — Procapsid Of Bacteriophage Phix174, Chain 1
Homologous superfamily homologous superfamily	10 — Scaffold protein D

Domain ID domain_id	1tx9B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1850 — Procapsid Of Bacteriophage Phix174, Chain 1
Homologous superfamily homologous superfamily	10 — Scaffold protein D

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Unit-cell length a length_a	106.440 Å
Unit-cell length b length_b	106.440 Å
Unit-cell length c length_c	127.019 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.310 Å
Low-resolution limit resolution_low	49.090 Å
R factor r_factor	0.2800
R_work r_work	0.2710
R_free r_free	0.3100

Description description	Scaffolding protein D
Molecular weight formula_weight	16822.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2125

gpd prior to capsid assembly

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

Scaffolding protein D

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

1tx9__assembly_1__model_1

1tx9__assembly_1__model_1 | I(q)

1tx9__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Enterobacteria phage phiX174
NCBI taxonomy ID ncbi_taxonomy_id	10847
Host organism host_organism	Escherichia coli BL21(DE3)

gpd prior to capsid assembly

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

Scaffolding protein D

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

1tx9__assembly_1__model_1

1tx9__assembly_1__model_1 | I(q)

1tx9__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)