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9vr2

The crystal structure of MetRS-like protein from Streptomyces candidus in complex with L-Glu and L-N6-OH-lysine

Method: X-RAY DIFFRACTION D_max: 127.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vr2
deposition_date	2025-07-05
last_revision	2026-05-13
title	The crystal structure of MetRS-like protein from Streptomyces candidus in complex with L-Glu and L-N6-OH-lysine
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	36.94 Å
rg_electron	37.09 Å
i0	418421000.00
molecular_weight	109510.0 kDa
excluded_volume	105040 Å³
envelope_volume	180380 Å³
shell_volume	43018 Å³
envelope_diameter	136.2 Å
shell_rg	40.49 Å
envelope_rg	37.01 Å
shape_rg	37.02 Å
total_rg	37.36 Å
total_atoms	8276
n_residues	1064
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	127.3 Å
rg_real	37.37 Å
rg_real_error	1.18 Å
i0_real	4.1840e+08
i0_real_error	6.9350e+06
rg_reciprocal	37.11 Å
i0_reciprocal	418300000.0000
total_estimate	0.6050
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	32.6 Å
skewness	0.606
kurtosis	-0.230
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	74570000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.691; Stabil: 1.000; Sysdev: 0.159; Positv: 1.000; Valcen: 0.676; Smooth: 0.635

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

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	8955

ENLSALAAVHAERREQAVERQGRPVLLLPSFPTPNGELHLGHLSGPFLNADACRRALLAAGERAHLLLGTVGHQSQVSAAAEAEGLSFHELAERNTDAIIEGLQAAGIDWDVFVRPSEPAYPAMATSVFESLRDRGVLVRRTEPTNYCEPCGRFLLEAFVAGHCPHCGSNQTAGIECELCALPYDDRDLVDPSCATCGAAATQRPLTRYFMPLEPLRDELSGYLRGAAMHGRLRAYTERVLAKTLPDLPVSIPAEHGIPIHVEDASGPAEQRMYSAFELAARFLTALDGFADGWEAYARQENPRTVLFFGFDNAFLRAFAFPAVLGAFTDALPLPEALVCNDFYLLDGEKFSTGRKHAVWARQAVTPANADQLRLYLAATSPDVRRRDFTTRGYAEFVTAELIGRWQRRLDDVGGRVAEHFGGLTPEAGGWHAEAERFYGQIKEFASCATLDYLPGRFKPRAVVAAACAFIRQAEDFAEVSADATPGSGIARTCAALELMALRTLAMAVWPLAPEFGRRVAAALGEDTIALEPTPRWVRPDTEIKFATDHFSPDEVVAGR

Source

organism	Streptomyces candidus
ncbi_taxonomy_id	67283
host_organism	Escherichia coli

Entity 2 non-polymer

description	N~6~-hydroxy-L-lysine
formula_weight	162.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	GLUTAMIC ACID
formula_weight	147.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	5

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	668

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6. Citations (1)

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length_a	101.583 Å
length_b	50.534 Å
length_c	106.613 Å
angle_alpha	90.00 °
angle_beta	89.82 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.450 Å
resolution_low	41.670 Å
r_factor	0.1746
r_work	0.1723
r_free	0.2179

fit	/app/data/saxs_computation/vr/9vr2/9vr2.fit
pddf	/app/data/pr_computation/vr/9vr2/9vr2.pr.out
profile	/app/data/saxs_computation/vr/9vr2/9vr2.dat