← Back to search

9vq4

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

Method: X-RAY DIFFRACTION D_max: 126.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9vq4
deposition_date	2025-07-04
last_revision	2026-05-13
title	The crystal structure of MetRs-like protein from Streptomyces candidus bound to D-Glu
keywords	Methionine-tRNA ligase, LIGASE; LIGASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	36.79 Å
rg_electron	36.57 Å
i0	215797000.00
molecular_weight	116340.0 kDa
excluded_volume	144430 Å³
envelope_volume	180160 Å³
shell_volume	42982 Å³
envelope_diameter	134.8 Å
shell_rg	40.59 Å
envelope_rg	36.28 Å
shape_rg	36.55 Å
total_rg	36.86 Å
total_atoms	8193
n_residues	1059
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	126.8 Å
rg_real	37.03 Å
rg_real_error	1.11 Å
i0_real	2.1580e+08
i0_real_error	3.5700e+06
rg_reciprocal	36.88 Å
i0_reciprocal	215800000.0000
total_estimate	0.6451
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	35.4 Å
skewness	0.515
kurtosis	-0.132
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	69010000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 0.159; Positv: 1.000; Valcen: 0.826; Smooth: 0.666

▶

4. Crystallography & Experiment

▶

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	A,B
atom_count	9063

ENLSALAAVHAERREQAVERQGRPVLLLPSFPTPNGELHLGHLSGPFLNADACRRALLAAGERAHLLLGTVGHQSQVSAAAEAEGLSFHELAERNTDAIIEGLQAAGIDWDVFVRPSEPAYPAMATSVFESLRDRGVLVRRTEPTNYCEPCGRFLLEAFVAGHCPHCGSNQTAGIECELCALPYDDRDLVDPSCATCGAAATQRPLTRYFMPLEPLRDELSGYLRGAAMHGRLRAYTERVLAKTLPDLPVSIPAEHGIPIHVEDASGPAEQRMYSAFELAARFLTALDGFADGWEAYARQENPRTVLFFGFDNAFLRAFAFPAVLGAFTDALPLPEALVCNDFYLLDGEKFSTGRKHAVWARQAVTPANADQLRLYLAATSPDVRRRDFTTRGYAEFVTAELIGRWQRRLDDVGGRVAEHFGGLTPEAGGWHAEAERFYGQIKEFASCATLDYLPGRFKPRAVVAAACAFIRQAEDFAEVSADATPGSGIARTCAALELMALRTLAMAVWPLAPEFGRRVAAALGEDTIALEPTPRWVRPDTEIKFATDHFSPDEVVAGR

Source

organism	Streptomyces candidus
ncbi_taxonomy_id	67283
host_organism	Escherichia coli

Entity 2 non-polymer

description	D-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	870

▶

6. Citations (1)

▶

length_a	101.236 Å
length_b	50.434 Å
length_c	106.322 Å
angle_alpha	90.00 °
angle_beta	90.23 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.000 Å
resolution_low	36.733 Å
r_factor	0.1740
r_work	0.1730
r_free	0.2101

fit	/app/data/saxs_computation/vq/9vq4/9vq4.fit
pddf	/app/data/pr_computation/vq/9vq4/9vq4.pr.out
profile	/app/data/saxs_computation/vq/9vq4/9vq4.dat