E.coli seryl-tRNA synthetase

Method: X-RAY DIFFRACTION D_max: 110.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qmp
deposition_date	2025-03-24
last_revision	2025-05-14
title	E.coli seryl-tRNA synthetase
keywords	aminoacyl-tRNA synthetase, ATP binding, TRANSLATION; TRANSLATION
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	27.95 Å
rg_electron	28.01 Å
i0	37780800.00
molecular_weight	46554.0 kDa
excluded_volume	57913 Å³
envelope_volume	75542 Å³
shell_volume	25229 Å³
envelope_diameter	115.6 Å
shell_rg	31.41 Å
envelope_rg	29.32 Å
shape_rg	28.02 Å
total_rg	28.35 Å
total_atoms	6526
n_residues	413
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	110.8 Å
rg_real	28.61 Å
rg_real_error	1.28 Å
i0_real	3.7780e+07
i0_real_error	6.4070e+05
rg_reciprocal	28.40 Å
i0_reciprocal	37770000.0000
total_estimate	0.7179
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	27.2 Å
skewness	0.908
kurtosis	0.681
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	5089000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.341; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.364; Smooth: 0.943

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (2)

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length_a	144.648 Å
length_b	90.720 Å
length_c	69.800 Å
angle_alpha	90.00 °
angle_beta	117.75 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.480 Å
resolution_low	19.020 Å
r_factor	0.1516
r_work	0.1497
r_free	0.1858

description	Serine--tRNA ligase
formula_weight	48478.0 kDa
ec_number	6.1.1.11
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	6662

E.coli seryl-tRNA synthetase

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	86

fit	/app/data/saxs_computation/qm/9qmp/9qmp.fit
pddf	/app/data/pr_computation/qm/9qmp/9qmp.pr.out
profile	/app/data/saxs_computation/qm/9qmp/9qmp.dat