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9ymm

;Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis in complex with 5'-O-(N-Glutamyl)sulfamoyladeonosine ;

Method: X-RAY DIFFRACTION D_max: 159.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ymm
deposition_date	2025-10-10
last_revision	2025-10-22
title	;Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis in complex with 5'-O-(N-Glutamyl)sulfamoyladeonosine ;
keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, Glutamate--tRNA ligase (GltX), LIGASE; LIGASE
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	49.37 Å
rg_electron	48.79 Å
i0	698740000.00
molecular_weight	218470.0 kDa
excluded_volume	272500 Å³
envelope_volume	407000 Å³
shell_volume	67469 Å³
envelope_diameter	164.2 Å
shell_rg	56.16 Å
envelope_rg	47.10 Å
shape_rg	48.78 Å
total_rg	49.09 Å
total_atoms	15316
n_residues	1897
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	159.3 Å
rg_real	49.15 Å
rg_real_error	1.31 Å
i0_real	6.9870e+08
i0_real_error	1.3890e+07
rg_reciprocal	49.37 Å
i0_reciprocal	698900000.0000
total_estimate	0.8952
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	69.7 Å
skewness	0.046
kurtosis	-0.701
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	38610000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.905

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Glutamate--tRNA ligase
formula_weight	58885.5 kDa
ec_number	6.1.1.17
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	15316

MAHHHHHHMGTLEAQTQGPGSMTRPVRTRIAPSPTGFPHVGTAYIALFNLVFAKSMGGEFILRIEDTDQVRSTKQSEQMILDALKWAGLSWAEGPDVGGPHAPYRQSERADIYKKYAEKLLDDGHAFRCFCTPEELDAMREAQMAAGLPVKYDGRYANLSREESDALVAQGKPFVIRMRVPSSGVCTIKDMLRGEVVIPWEQVDMQVLLKTDGLPTYHLANVVDDHLMQITHVLRGEEWLPSAPKHQLLYEYFGWQMPELCHMPLLRNPDKSKLSKRKNPTSITYYRDAGILPEALMNYLGRMGYSLPNEQEKFTLDEMIQSFDIQRISLGGPVFDIEKLYWLNGEYLRTLSVDDLKNKILAWASDDTKLTAIARAIQPRINLLSDAINWAGFYFQNLPAITAEDFAHKSLDNEQILEILYLATWQLENLPIWSEENIYQTLKGLAAHFDIKLKDFMQPFFVAIAGSTSSTPVMNSMYIIGADMTLARLRHACEILGGLGKKKLKKLEEKNKSLPNFLA

Source

organism	Moraxella catarrhalis
ncbi_taxonomy_id	480
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE
formula_weight	475.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	40

Entity 4 non-polymer

description	HEXAETHYLENE GLYCOL
formula_weight	282.3 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	NONAETHYLENE GLYCOL
formula_weight	414.5 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	53.713 Å
length_b	124.225 Å
length_c	458.212 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.920 Å
resolution_low	49.300 Å
r_factor	0.2164
r_work	0.2145
r_free	0.2526

fit	/app/data/saxs_computation/ym/9ymm/9ymm.fit
pddf	/app/data/pr_computation/ym/9ymm/9ymm.pr.out
profile	/app/data/saxs_computation/ym/9ymm/9ymm.dat