← Back to search

9qm6

Crystal structure of highly stable methionine gamma-lyase from Thermobrachium celere in complex with PLP and norleucine

Method: X-RAY DIFFRACTION D_max: 163.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qm6
deposition_date	2025-03-21
last_revision	2025-11-19
title	Crystal structure of highly stable methionine gamma-lyase from Thermobrachium celere in complex with PLP and norleucine
keywords	Enzyme, methionine gamma-lyase, complex, PLP, inhibitor, LYASE; LYASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	46.54 Å
rg_electron	46.91 Å
i0	444600000.00
molecular_weight	176020.0 kDa
excluded_volume	221210 Å³
envelope_volume	294520 Å³
shell_volume	55839 Å³
envelope_diameter	161.1 Å
shell_rg	46.98 Å
envelope_rg	46.71 Å
shape_rg	46.94 Å
total_rg	46.83 Å
total_atoms	24749
n_residues	1597
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	163.6 Å
rg_real	47.08 Å
rg_real_error	1.78 Å
i0_real	4.4460e+08
i0_real_error	9.0500e+06
rg_reciprocal	46.55 Å
i0_reciprocal	444300000.0000
total_estimate	0.8045
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	38.5 Å
skewness	0.506
kurtosis	-0.534
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	53650000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.653; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.789; Smooth: 0.706

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	L-methionine gamma-lyase
formula_weight	45939.3 kDa
ec_number	4.4.1.11
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	24756

MGSSHHHHHHSSGLVPRGSHMDREFAKNMGFSTKAIHAGNHKNEFGTLATPIYQTATFVFDSAQQGGNRFAGKEEGYIYTRLGNPTVTVLEEKIAILEGGEACVATSSGMGAISSALWTALKAGDHVVAADTLYGCTFAYLSHGLTRYGVEVTFVDASNPENIKEAMRPNTKAIYIETPANPNLKLIDIKKVAEIAHSKEDCILIVDNTFCTPYIQRPIELGADVVVHSATKFLNGHGDVIAGFVVGRKSFIDQVRLYGIKDMTGACLSPFDAYLILRGLKTLEIRMERHCSNAMKVAKFLEEHKAVKKVYYPGLESFEQYELAKEQMKLPGAIIAFELNGGVEEGIKVLNSCKVCTLAVSLGDAETLIQHPASMTHSPYTREERLKAGISDGLIRLAVGLENAEDIIADLKQALDAII

Source

organism	Thermobrachium celere
ncbi_taxonomy_id	53422
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	NORLEUCINE
formula_weight	131.2 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	7

▶

6. Citations (1)

▶

length_a	86.426 Å
length_b	86.426 Å
length_c	862.410 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	48

space_group	P 61 2 2
int_tables_number	178
crystal_system	—

resolution	2.607 Å
resolution_low	37.840 Å
r_factor	0.2507
r_work	0.2498
r_free	0.2678

fit	/app/data/saxs_computation/qm/9qm6/9qm6.fit
pddf	/app/data/pr_computation/qm/9qm6/9qm6.pr.out
profile	/app/data/saxs_computation/qm/9qm6/9qm6.dat

Crystal structure of highly stable methionine gamma-lyase from Thermobrachium celere in complex with PLP and norleucine

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