Crystal structure of Yarrowia lipolytica methionine gamma-lyase in complex with L-methionine

Method: X-RAY DIFFRACTION D_max: 96.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uuw
deposition_date	2025-05-08
last_revision	2026-05-13
title	Crystal structure of Yarrowia lipolytica methionine gamma-lyase in complex with L-methionine
keywords	PLP, Methionine, 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	28.63 Å
rg_electron	27.92 Å
i0	100298000.00
molecular_weight	79448.0 kDa
excluded_volume	99604 Å³
envelope_volume	118830 Å³
shell_volume	35651 Å³
envelope_diameter	101.8 Å
shell_rg	35.16 Å
envelope_rg	28.00 Å
shape_rg	27.93 Å
total_rg	28.61 Å
total_atoms	5613
n_residues	712
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	96.3 Å
rg_real	28.65 Å
rg_real_error	0.71 Å
i0_real	1.0030e+08
i0_real_error	1.5090e+06
rg_reciprocal	28.64 Å
i0_reciprocal	100300000.0000
total_estimate	0.8681
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.5 Å
skewness	0.416
kurtosis	-0.211
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	44640000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.852

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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	166.054 Å
length_b	166.054 Å
length_c	81.314 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	3.040 Å
resolution_low	70.782 Å
r_factor	0.2344
r_work	0.2327
r_free	0.2662

description	Cys/Met metabolism PLP-dependent enzyme-domain-containing protein
formula_weight	42203.2 kDa
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	5613

Crystal structure of Yarrowia lipolytica methionine gamma-lyase in complex with L-methionine

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Yarrowia lipolytica
ncbi_taxonomy_id	4952
host_organism	Escherichia coli

description	METHIONINE
formula_weight	149.2 kDa
src_method	syn
entity_count	2

fit	/app/data/saxs_computation/uu/9uuw/9uuw.fit
pddf	/app/data/pr_computation/uu/9uuw/9uuw.pr.out
profile	/app/data/saxs_computation/uu/9uuw/9uuw.dat