← Back to search

9vsm

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

Method: X-RAY DIFFRACTION D_max: 157.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9vsm
deposition_date	2025-07-09
title	;Crystal structure of cystathionine gamma-synthase from Lactobacillus plantarum complexed with the cystathionine-bound external aldimine ;
keywords	cystathionine gamma-synthase, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	45.61 Å
rg_electron	45.88 Å
i0	384407000.00
molecular_weight	161830.0 kDa
excluded_volume	202690 Å³
envelope_volume	274930 Å³
shell_volume	52501 Å³
envelope_diameter	169.0 Å
shell_rg	47.24 Å
envelope_rg	45.04 Å
shape_rg	45.88 Å
total_rg	45.94 Å
total_atoms	11415
n_residues	1477
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	157.2 Å
rg_real	46.05 Å
rg_real_error	1.95 Å
i0_real	3.8440e+08
i0_real_error	7.9790e+06
rg_reciprocal	45.61 Å
i0_reciprocal	384200000.0000
total_estimate	0.5792
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	35.9 Å
skewness	0.467
kurtosis	-0.552
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	46720000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.683; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.607; Smooth: 0.684

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Cysteine gamma synthase/O-succinylhomoserine (Thiol)-lyase
formula_weight	41566.7 kDa
ec_number	2.5.1.48
mutation	K203A
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	13111

MTKQAEKLHIETRLAQAGNRSDDEKTGAISAPIYLSTAYRHAGLGQSTGFDYPREAQPTRCILERVLAEMEHGIAAYALTSGMAAIQLVFTLFNSGDKIIVSDDLYGGSYRFFDLLHDHYHLDFAVWDGQDQATLAALADDQTVALWLETPSNPTMKVIDITATAATAHAHDLKLIVDNTFYTPLIQKPLDLGADIVVHSATAYLAGHNDVLAGAVVVKSQADADALEFNLVTTGAVLDPFDAWLLLRSLKTLPLRLHQQEANAQELVTVLEADEHVERVLYSGRGGMISFYLATGTDVDTFLRALNVISFAESLGGVESLLTVPAVQTHADLTEEQRQSKGITANLLRLSVGIENSADLAADLKQALIRATKLEHHHHHH

Source

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

Entity 2 non-polymer

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 ;
formula_weight	451.4 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1500

▶

6. Citations (1)

▶

length_a	155.987 Å
length_b	110.656 Å
length_c	107.388 Å
angle_alpha	90.00 °
angle_beta	111.99 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.580 Å
resolution_low	46.790 Å
r_factor	0.1518
r_work	0.1508
r_free	0.1707

fit	/app/data/saxs_computation/vs/9vsm/9vsm.fit
pddf	/app/data/pr_computation/vs/9vsm/9vsm.pr.out
profile	/app/data/saxs_computation/vs/9vsm/9vsm.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction