SAXSdb — 6sld

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

CRAL-TRIO domain-containing protein YKL091C

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;(1R)-2-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YKJ1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–307； UniProt 4–310

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	6sld
Deposition date deposition_date	2019-08-19
Structure title title	Structure of the Phosphatidylcholine Binding Mutant of Yeast Sec14 Homolog Sfh1 (S175I,T177I) in Complex with Phosphatidylinositol
Keywords keywords	Sec14, Sfh1, Phosphatidylcholine, Phosphatidylinositol, LIPID TRANSPORT; LIPID TRANSPORT
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.

6sld__assembly_1__model_1

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

Download this curve (.dat)

6sld__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6sld__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.33 Å
Rg (electron density)	19.22 Å
Total Rg	20.29 Å
Atom count	5193
Residues	307
Excluded volume	46682 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6sld__assembly_1__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	CRAL-TRIO domain-containing protein YKL091C
Molecular weight formula_weight	35825.1 kDa
Mutation mutation	S175I,T177I
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5598

SILDTYPQICSPNALPGTPGNLTKEQEEALLQFRSILLEKNYKERLDDSTLLRFLRARKFDINASVEMFVETERWREEYGANTIIEDYENNKEAEDKERIKLAKMYPQYYHHVDKDGRPLYFEELGGINLKKMYKITTEKQMLRNLVKEYELFATYRVPACSRRAGYLIETICIVLDLKGISLSNAYHVLSYIKDVADISQNYYPERMGKFYIIHSPFGFSTMFKMVKPFLDPVTVSKIFILGSSYKKELLKQIPIENLPVKYGGTSVLHNPNDKFYYSDIGPWRDPRYIGPEGEIPNIFGKFTVTS

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;(1R)-2-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate ;
Molecular weight formula_weight	865.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	391

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6slda1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.3 — CRAL/TRIO N-terminal domain
Family Family family	a.5.3.0 — automated matches

Domain ID domain_id	d6slda2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.13 — SpoIIaa-like
Superfamily Superfamily superfamily	c.13.1 — CRAL/TRIO domain
Family Family family	c.13.1.0 — automated matches

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Unit-cell length a length_a	48.220 Å
Unit-cell length b length_b	70.810 Å
Unit-cell length c length_c	90.190 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	45.095 Å
R factor r_factor	0.1445
R_work r_work	0.1435
R_free r_free	0.1635

Structure of the Phosphatidylcholine Binding Mutant of Yeast Sec14 Homolog Sfh1 (S175I,T177I) in Complex with Phosphatidylinositol

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

CRAL-TRIO domain-containing protein YKL091C

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

6sld__assembly_1__model_1

6sld__assembly_1__model_1 | I(q)

6sld__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Structure of the Phosphatidylcholine Binding Mutant of Yeast Sec14 Homolog Sfh1 (S175I,T177I) in Complex with Phosphatidylinositol

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

CRAL-TRIO domain-containing protein YKL091C

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

6sld__assembly_1__model_1

6sld__assembly_1__model_1 | I(q)

6sld__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)