← Back to search

9qur

Crystal structure of gamma-Glutamyl-Methylamide Synthetase from Methylovorus mays (MmGmaS) in complex with ATPgS

Method: X-RAY DIFFRACTION D_max: 163.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qur
deposition_date	2025-04-11
last_revision	2026-01-28
title	Crystal structure of gamma-Glutamyl-Methylamide Synthetase from Methylovorus mays (MmGmaS) in complex with ATPgS
keywords	Ligase, Complex, ATP-dependent; LIGASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	49.11 Å
rg_electron	48.83 Å
i0	1300920000.00
molecular_weight	297540.0 kDa
excluded_volume	370570 Å³
envelope_volume	504220 Å³
shell_volume	85540 Å³
envelope_diameter	162.2 Å
shell_rg	53.54 Å
envelope_rg	47.55 Å
shape_rg	48.84 Å
total_rg	48.96 Å
total_atoms	20926
n_residues	2669
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	163.1 Å
rg_real	48.98 Å
rg_real_error	1.24 Å
i0_real	1.3010e+09
i0_real_error	2.3050e+07
rg_reciprocal	49.11 Å
i0_reciprocal	1301000000.0000
total_estimate	0.8899
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	61.2 Å
skewness	0.213
kurtosis	-0.499
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	114700000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.873

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Glutamate--methylamine ligase
formula_weight	49258.6 kDa
ec_number	6.3.4.12,6.3.1.6
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	21045

GSHMESLEEAQKFLEDHHVKYVLAQFVDIHGVAKVKSVPASHLNDILTTGAGFAGGAIWGTGIAPNGPDYMAIGELSTLSLIPWQPGYARLVCDGHVNGKPYEFDTRVVLKQQIARLAEKGWTLYTGLEPEFSLLKKDEHGAVHPFDDSDTLQKPCYDYKGITRHSPFLEKLTESLVEVGLDIYQIDHEDANGQFEINYTYADCLKSADDYIMFKMAASEIANELGIICSFMPKPFSNRPGNGMHMHMSIGDGKKSLFQDDSDPSGLGLSKLAYHFLGGILAHAPALAAVCAPTVNSYKRLVVGRSLSGATWAPAYIAYGNNNRSTLVRIPYGRLELRLPDGSCNPYLATAAVIAAGLDGVARELDPGTGRDDNLYDYSLEQLAEFGIGILPQNLGEALDALEADQVIMDAMGPGLSKEFVELKRMEWVDYMRHVSDWEINRYVQFY

Source

organism	Methylovorus mays
ncbi_taxonomy_id	184077
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
formula_weight	523.2 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	18

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	103

▶

6. Citations (1)

▶

length_a	141.740 Å
length_b	246.923 Å
length_c	105.760 Å
angle_alpha	90.00 °
angle_beta	111.17 °
angle_gamma	90.00 °
z_pdb	24

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.650 Å
resolution_low	90.890 Å
r_factor	0.2255
r_work	0.2248
r_free	0.2597

fit	/app/data/saxs_computation/qu/9qur/9qur.fit
pddf	/app/data/pr_computation/qu/9qur/9qur.pr.out
profile	/app/data/saxs_computation/qu/9qur/9qur.dat

Crystal structure of gamma-Glutamyl-Methylamide Synthetase from Methylovorus mays (MmGmaS) in complex with ATPgS

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