Crystal structure of Staphylococcus aureus cystathionine gamma-lyase V129G

Method: X-RAY DIFFRACTION D_max: 64.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xlu
deposition_date	2025-11-08
title	Crystal structure of Staphylococcus aureus cystathionine gamma-lyase V129G
keywords	cystathionine gamma-lyase, PLP-dependent enzyme, transsulfuration, Staphylococcus aureus, LYASE; LYASE
method	X-RAY DIFFRACTION

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	20.72 Å
rg_electron	19.63 Å
i0	21945900.00
molecular_weight	36324.0 kDa
excluded_volume	45794 Å³
envelope_volume	52501 Å³
shell_volume	21965 Å³
envelope_diameter	65.5 Å
shell_rg	26.45 Å
envelope_rg	19.81 Å
shape_rg	19.62 Å
total_rg	20.57 Å
total_atoms	2556
n_residues	337
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

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3. P(r) Analysis (GNOM)

dmax	64.8 Å
rg_real	20.61 Å
rg_real_error	0.35 Å
i0_real	2.1950e+07
i0_real_error	2.9200e+05
rg_reciprocal	20.63 Å
i0_reciprocal	21950000.0000
total_estimate	0.9005
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	26.3 Å
skewness	0.174
kurtosis	-0.430
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	4852000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	62.832 Å
length_b	80.467 Å
length_c	161.067 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 2 2 2
int_tables_number	23
crystal_system	orthorhombic

resolution	2.330 Å
resolution_low	40.270 Å
r_factor	0.2123
r_work	0.2071
r_free	0.2603

description	Cystathionine gamma-synthase homolog
formula_weight	43294.8 kDa
mutation	V129G
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	2782

Crystal structure of Staphylococcus aureus cystathionine gamma-lyase V129G

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Staphylococcus aureus subsp. aureus Mu50
ncbi_taxonomy_id	158878
host_organism	Escherichia coli BL21(DE3)

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	226

fit	/app/data/saxs_computation/xl/9xlu/9xlu.fit
pddf	/app/data/pr_computation/xl/9xlu/9xlu.pr.out
profile	/app/data/saxs_computation/xl/9xlu/9xlu.dat