SAXSdb — 8guh

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

Serine palmitoyltransferase

Sphingobacterium multivorum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	[4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate × 2 1,2-ETHANEDIOL × 12 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A7BFV6_SPHMU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–399； UniProt 1–399

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	8guh
Deposition date deposition_date	2022-09-12
Structure title title	Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Tris
Keywords keywords	transferase, sphingolipid; TRANSFERASE
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.

8guh__assembly_1__model_1

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

Download this curve (.dat)

8guh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8guh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.04 Å
Rg (electron density)	26.02 Å
Total Rg	26.80 Å
Atom count	6164
Residues	788
Excluded volume	110200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8guh__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 (4)

Entity 1 Entity 1 polymer

Description description	Serine palmitoyltransferase
Molecular weight formula_weight	43822.9 kDa
EC 编号 ec_number	2.3.1.50
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	3686

MSKGKLGEKISQFKIVEELKAKGLYAYFRPIQSKQDTEVKIDGRRVLMFGSNSYLGLTTDTRIIKAAQDALEKYGTGCAGSRFLNGTLDIHVELEEKLSAYVGKEAAILFSTGFQSNLGPLSCLMGRNDYILLDERDHASIIDGSRLSFSKVIKYGHNNMEDLRAKLSRLPEDSAKLICTDGIFSMEGDIVNLPELTSIANEFDAAVMVDDAHSLGVIGHKGAGTASHFGLNDDVDLIMGTFSKSLASLGGFVAGDADVIDFLKHNARSVMFSASMTPASVASTLKALEIIQNEPEHIEKLWKNTDYAKAQLLDHGFDLGATESPILPIFIRSNEKTFWVTKMLQDDGVFVNPVVSPAVPAEESLIRFSLMATHTYDQIDEAIEKMVKVFKQAEVETLI

Source Source

Source organism organism	Sphingobacterium multivorum
NCBI taxonomy ID ncbi_taxonomy_id	28454
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	[4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate
Molecular weight formula_weight	350.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	456

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Unit-cell length a length_a	61.321 Å
Unit-cell length b length_b	61.321 Å
Unit-cell length c length_c	208.573 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	8

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

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	46.031 Å
R factor r_factor	—
R_work r_work	0.1695
R_free r_free	0.2143

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Tris

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

Serine palmitoyltransferase

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

8guh__assembly_1__model_1

8guh__assembly_1__model_1 | I(q)

8guh__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Tris

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

Serine palmitoyltransferase

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

8guh__assembly_1__model_1

8guh__assembly_1__model_1 | I(q)

8guh__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)