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9zpg

Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis (Apo)

Method: X-RAY DIFFRACTION D_max: 151.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zpg
deposition_date	2025-12-16
last_revision	2025-12-24
title	Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis (Apo)
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	41.55 Å
rg_electron	41.58 Å
i0	184246000.00
molecular_weight	110170.0 kDa
excluded_volume	137820 Å³
envelope_volume	193130 Å³
shell_volume	42006 Å³
envelope_diameter	152.6 Å
shell_rg	42.11 Å
envelope_rg	41.85 Å
shape_rg	41.56 Å
total_rg	41.67 Å
total_atoms	7739
n_residues	988
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	151.6 Å
rg_real	42.05 Å
rg_real_error	2.11 Å
i0_real	1.8420e+08
i0_real_error	3.7050e+06
rg_reciprocal	41.55 Å
i0_reciprocal	184100000.0000
total_estimate	0.7723
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	35.9 Å
skewness	0.626
kurtosis	-0.248
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	15860000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.542; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.678; Smooth: 0.731

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Glutamate--tRNA ligase
formula_weight	58885.5 kDa
ec_number	6.1.1.17
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7739

MAHHHHHHMGTLEAQTQGPGSMTRPVRTRIAPSPTGFPHVGTAYIALFNLVFAKSMGGEFILRIEDTDQVRSTKQSEQMILDALKWAGLSWAEGPDVGGPHAPYRQSERADIYKKYAEKLLDDGHAFRCFCTPEELDAMREAQMAAGLPVKYDGRYANLSREESDALVAQGKPFVIRMRVPSSGVCTIKDMLRGEVVIPWEQVDMQVLLKTDGLPTYHLANVVDDHLMQITHVLRGEEWLPSAPKHQLLYEYFGWQMPELCHMPLLRNPDKSKLSKRKNPTSITYYRDAGILPEALMNYLGRMGYSLPNEQEKFTLDEMIQSFDIQRISLGGPVFDIEKLYWLNGEYLRTLSVDDLKNKILAWASDDTKLTAIARAIQPRINLLSDAINWAGFYFQNLPAITAEDFAHKSLDNEQILEILYLATWQLENLPIWSEENIYQTLKGLAAHFDIKLKDFMQPFFVAIAGSTSSTPVMNSMYIIGADMTLARLRHACEILGGLGKKKLKKLEEKNKSLPNFLA

Source

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

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	12

Entity 3 non-polymer

description	HEXAETHYLENE GLYCOL
formula_weight	282.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	103.557 Å
length_b	53.602 Å
length_c	127.962 Å
angle_alpha	90.00 °
angle_beta	108.19 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.750 Å
resolution_low	47.070 Å
r_factor	0.2177
r_work	0.2154
r_free	0.2613

fit	/app/data/saxs_computation/zp/9zpg/9zpg.fit
pddf	/app/data/pr_computation/zp/9zpg/9zpg.pr.out
profile	/app/data/saxs_computation/zp/9zpg/9zpg.dat

Crystal structure of Glutamate--tRNA ligase (GltX) from Moraxella catarrhalis (Apo)

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