SAXSdb — 6cbc

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

Vacuolar protein sorting-associated protein

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

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	G0S3B8_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–329； UniProt 2–335 Author chain B； PDBConstruct 2–329； UniProt 2–335

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	6cbc
Deposition date deposition_date	2018-02-02
Structure title title	Crystal structure of an N-terminal fragment of Vps13.
Keywords keywords	Lipid transfer protein, Membrane trafficking, Endoplasmic reticulum, Mitochondria, Endosomes, LIPID BINDING PROTEIN; LIPID BINDING 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.

6cbc__assembly_1__model_1

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

Download this curve (.dat)

6cbc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6cbc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.37 Å
Rg (electron density)	27.41 Å
Total Rg	28.14 Å
Atom count	4003
Residues	508
Excluded volume	71806 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6cbc__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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Unit-cell length a length_a	58.933 Å
Unit-cell length b length_b	85.984 Å
Unit-cell length c length_c	71.027 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	48.543 Å
R factor r_factor	0.2317
R_work r_work	0.2301
R_free r_free	0.2642

Description description	Vacuolar protein sorting-associated protein
Molecular weight formula_weight	39234.5 kDa
Mutation mutation	P228H, P236E
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	4003

Crystal structure of an N-terminal fragment of Vps13.

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

Vacuolar protein sorting-associated 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

6cbc__assembly_1__model_1

6cbc__assembly_1__model_1 | I(q)

6cbc__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

7. Citations (1)

Source organism organism	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism host_organism	Escherichia coli

Crystal structure of an N-terminal fragment of Vps13.

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

Vacuolar protein sorting-associated 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

6cbc__assembly_1__model_1

6cbc__assembly_1__model_1 | I(q)

6cbc__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

7. Citations (1)