← Back to search

9shc

Structure of Streptococcus pneumoniae methionyl-tRNA synthetase bound to the sulphamoyl analogue of methionyl-adenylate

Method: X-RAY DIFFRACTION D_max: 104.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9shc
deposition_date	2025-08-26
last_revision	2025-09-24
title	Structure of Streptococcus pneumoniae methionyl-tRNA synthetase bound to the sulphamoyl analogue of methionyl-adenylate
keywords	aminoacyl-tRNA synthetase, RNA BINDING PROTEIN; RNA BINDING PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	27.42 Å
rg_electron	26.99 Å
i0	99277400.00
molecular_weight	53530.0 kDa
excluded_volume	52322 Å³
envelope_volume	88430 Å³
shell_volume	28576 Å³
envelope_diameter	111.0 Å
shell_rg	32.90 Å
envelope_rg	27.62 Å
shape_rg	26.96 Å
total_rg	27.48 Å
total_atoms	4063
n_residues	498
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	104.8 Å
rg_real	27.65 Å
rg_real_error	1.07 Å
i0_real	9.9280e+07
i0_real_error	1.4920e+06
rg_reciprocal	27.58 Å
i0_reciprocal	99270000.0000
total_estimate	0.6223
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	28.9 Å
skewness	0.601
kurtosis	0.053
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	15780000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.544; Stabil: 1.000; Sysdev: 0.267; Positv: 1.000; Valcen: 0.719; Smooth: 0.935

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Methionine--tRNA ligase
formula_weight	75733.9 kDa
ec_number	6.1.1.10
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4129

MSEKNFYITTPIYYPSGKLHIGSAYTTIACDVLARYKRLMGYDVFYLTGLDEHGQKIQQKAEEAGITPQAYVDGMAVGVKELWQLLDISYDKFIRTTDDYHEKVVAQVFERLLAQDDIYLGEYSGWYSVSDEEFFTESQLAEVFRDEAGNVTGGIAPSGHEVEWVSEESYFLRLSKYQDRLVEFFKAHPEFITPDGRLNEMLRNFIEPGLEDLAVSRTTFTWGVPVPSNPKHVVYVWIDALLNYATALGYAQDEHGNFDKFWNGTVFHMVGKDILRFHSIYWPILLMMLDVKLPDRLIAHGWFVMKDGKMSKSKGNVVYPEMLVERYGLDPLRYYLMRNLPVGSDGTFTPEDYVGRINYELANDLGNLLNRTVSMINKYFDGQIPAYVEGVTEFDHVLAEVAEQSIADFHTHMEAVDYPRALEAVWTLISRTNKYIDETAPWVLAKDEALRDQLASVMSHLAASIRVVAHLIEPFMMETSRAVLTQLGLEEVSSLENLSLADFPADVTVVAKGTPIFPRLNMEEEIAYIKEQMEGNKPAVEKEWNPDEVELKLNKDEIKFEDFDKVEIRVAEVKEVSKVEGSDKLLQFRLDAGDGEDRQILSGIAKYYPNEQELVGKKVQIVANLKPRKMMKKYVSQGMILSAEHDGKLTLLTVDPAVPNGSVIG

Source

organism	Streptococcus pneumoniae
ncbi_taxonomy_id	1313
host_organism	Escherichia coli

Entity 2 non-polymer

description	;[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methylsulfanyl-butanoyl]sulfamate ;
formula_weight	477.5 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	48

▶

6. Citations (1)

▶

length_a	150.365 Å
length_b	72.888 Å
length_c	78.881 Å
angle_alpha	90.00 °
angle_beta	117.42 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.300 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.2083
r_free	0.2471

fit	/app/data/saxs_computation/sh/9shc/9shc.fit
pddf	/app/data/pr_computation/sh/9shc/9shc.pr.out
profile	/app/data/saxs_computation/sh/9shc/9shc.dat

Structure of Streptococcus pneumoniae methionyl-tRNA synthetase bound to the sulphamoyl analogue of methionyl-adenylate

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