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9vqj

The crystal structure of MetRs-like protein from Streptomyces candidus bound to L-Glu

Method: X-RAY DIFFRACTION D_max: 130.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vqj
deposition_date	2025-07-04
last_revision	2026-05-13
title	The crystal structure of MetRs-like protein from Streptomyces candidus bound to L-Glu
keywords	Methionine-tRNA ligase, 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	37.18 Å
rg_electron	37.11 Å
i0	217343000.00
molecular_weight	117080.0 kDa
excluded_volume	145300 Å³
envelope_volume	178240 Å³
shell_volume	42662 Å³
envelope_diameter	139.4 Å
shell_rg	40.37 Å
envelope_rg	37.01 Å
shape_rg	37.08 Å
total_rg	37.40 Å
total_atoms	8245
n_residues	1065
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	130.7 Å
rg_real	37.62 Å
rg_real_error	1.71 Å
i0_real	2.1730e+08
i0_real_error	3.8690e+06
rg_reciprocal	37.35 Å
i0_reciprocal	217300000.0000
total_estimate	0.6007
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	33.4 Å
skewness	0.613
kurtosis	-0.211
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	76260000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.639; Stabil: 0.998; Sysdev: 0.159; Positv: 1.000; Valcen: 0.626; Smooth: 0.792

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Methionine-tRNA ligase
formula_weight	61177.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	8991

ENLSALAAVHAERREQAVERQGRPVLLLPSFPTPNGELHLGHLSGPFLNADACRRALLAAGERAHLLLGTVGHQSQVSAAAEAEGLSFHELAERNTDAIIEGLQAAGIDWDVFVRPSEPAYPAMATSVFESLRDRGVLVRRTEPTNYCEPCGRFLLEAFVAGHCPHCGSNQTAGIECELCALPYDDRDLVDPSCATCGAAATQRPLTRYFMPLEPLRDELSGYLRGAAMHGRLRAYTERVLAKTLPDLPVSIPAEHGIPIHVEDASGPAEQRMYSAFELAARFLTALDGFADGWEAYARQENPRTVLFFGFDNAFLRAFAFPAVLGAFTDALPLPEALVCNDFYLLDGEKFSTGRKHAVWARQAVTPANADQLRLYLAATSPDVRRRDFTTRGYAEFVTAELIGRWQRRLDDVGGRVAEHFGGLTPEAGGWHAEAERFYGQIKEFASCATLDYLPGRFKPRAVVAAACAFIRQAEDFAEVSADATPGSGIARTCAALELMALRTLAMAVWPLAPEFGRRVAAALGEDTIALEPTPRWVRPDTEIKFATDHFSPDEVVAGR

Source

organism	Streptomyces candidus
ncbi_taxonomy_id	67283
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLUTAMIC ACID
formula_weight	147.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	739

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6. Citations (1)

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length_a	106.518 Å
length_b	50.290 Å
length_c	114.127 Å
angle_alpha	90.00 °
angle_beta	92.52 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.956 Å
resolution_low	49.358 Å
r_factor	0.1679
r_work	0.1669
r_free	0.2128

fit	/app/data/saxs_computation/vq/9vqj/9vqj.fit
pddf	/app/data/pr_computation/vq/9vqj/9vqj.pr.out
profile	/app/data/saxs_computation/vq/9vqj/9vqj.dat