SAXSdb — 9vsm

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

Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase

Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	;(2~{S})-4-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid ; × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	;(2~{S})-4-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid ; × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	F9URD2_LACPL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–373； UniProt 1–373 Author chain B； PDBConstruct 1–373； UniProt 1–373 Author chain C； PDBConstruct 1–373； UniProt 1–373 Author chain D； PDBConstruct 1–373； UniProt 1–373

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	9vsm
Deposition date deposition_date	2025-07-09
Structure title title	Crystal structure of cystathionine gamma-synthase from Lactobacillus plantarum complexed with the cystathionine-bound external aldimine
Keywords keywords	cystathionine gamma-synthase, TRANSFERASE; 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.

9vsm__assembly_1__model_1

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

Download this curve (.dat)

9vsm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vsm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.83 Å
Rg (electron density)	32.90 Å
Total Rg	33.43 Å
Atom count	11386
Residues	1474
Excluded volume	202240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vsm__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9vsm__assembly_2__model_1`	tetrameric （4）	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	Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
Molecular weight formula_weight	41566.7 kDa
EC 编号 ec_number	2.5.1.48
Mutation mutation	K203A
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	13111

MTKQAEKLHIETRLAQAGNRSDDEKTGAISAPIYLSTAYRHAGLGQSTGFDYPREAQPTRCILERVLAEMEHGIAAYALTSGMAAIQLVFTLFNSGDKIIVSDDLYGGSYRFFDLLHDHYHLDFAVWDGQDQATLAALADDQTVALWLETPSNPTMKVIDITATAATAHAHDLKLIVDNTFYTPLIQKPLDLGADIVVHSATAYLAGHNDVLAGAVVVKSQADADALEFNLVTTGAVLDPFDAWLLLRSLKTLPLRLHQQEANAQELVTVLEADEHVERVLYSGRGGMISFYLATGTDVDTFLRALNVISFAESLGGVESLLTVPAVQTHADLTEEQRQSKGITANLLRLSVGIENSADLAADLKQALIRATKLEHHHHHH

Source Source

Source organism organism	Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
NCBI taxonomy ID ncbi_taxonomy_id	220668
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;(2~{S})-4-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid ;
Molecular weight formula_weight	451.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1500

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Unit-cell length a length_a	155.987 Å
Unit-cell length b length_b	110.656 Å
Unit-cell length c length_c	107.388 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.99 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.580 Å
Low-resolution limit resolution_low	46.790 Å
R factor r_factor	0.1518
R_work r_work	0.1508
R_free r_free	0.1707

Crystal structure of cystathionine gamma-synthase from Lactobacillus plantarum complexed with the cystathionine-bound external aldimine

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

Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase

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

9vsm__assembly_1__model_1

9vsm__assembly_1__model_1 | I(q)

9vsm__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

7. Citations (1)

Crystal structure of cystathionine gamma-synthase from Lactobacillus plantarum complexed with the cystathionine-bound external aldimine

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

Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase

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

9vsm__assembly_1__model_1

9vsm__assembly_1__model_1 | I(q)

9vsm__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

7. Citations (1)