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9wqy

aminoacyl-tRNA-dependent peptide synthase, Sba18, complexed with streptothrisamine

Method: X-RAY DIFFRACTION D_max: 68.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wqy
deposition_date	2025-09-11
title	aminoacyl-tRNA-dependent peptide synthase, Sba18, complexed with streptothrisamine
keywords	aminoacyl-tRNA-dependent peptide synthase, Sba18, TRANSFERASE; TRANSFERASE
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	20.39 Å
rg_electron	19.54 Å
i0	33694800.00
molecular_weight	29378.0 kDa
excluded_volume	28103 Å³
envelope_volume	46085 Å³
shell_volume	19952 Å³
envelope_diameter	69.3 Å
shell_rg	25.69 Å
envelope_rg	19.73 Å
shape_rg	19.52 Å
total_rg	20.19 Å
total_atoms	2233
n_residues	285
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	68.3 Å
rg_real	20.36 Å
rg_real_error	0.46 Å
i0_real	3.3690e+07
i0_real_error	4.7070e+05
rg_reciprocal	20.37 Å
i0_reciprocal	33690000.0000
total_estimate	0.8765
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.4 Å
skewness	0.368
kurtosis	-0.254
angular_range	— – 0.3900 Å⁻¹
current_alpha	0.0000
highest_alpha	8544000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.803; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.985

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	aminoacyl-tRNA-dependent peptide synthase
formula_weight	34148.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2456

MRGSHHHHHHGSACELLRLIMHTDSTADVRDEADVPAEDFHQSAGRFRLLSGRGDPVRLLRAGRPGGRWAAALLEDGGQDGWFMWKGPAGHPDPELLSALLTGVSRLGPATLVLLPEWDFPEVLAAAGYRPAPRYATGLVPTGGGDEAILARMRPSTRSRVRRALRSGLEFADDPGRIDEFYDFYAPAMIRANSPDLAPLDLLHDLLAHPSVHLFTALHEGRVAAGSICFRNRNSLEARFVATHPEHRVDGSMNFVHFQTIRRAAAEGLEHFDLSGISTGEVDGKTAGINRFKLGFGGEVLHYPTYATRSGD

Source

organism	Streptomyces sp.
ncbi_taxonomy_id	1931
host_organism	Escherichia coli M15

Entity 2 non-polymer

description	streptothrisamine
formula_weight	374.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	196

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6. Citations (1)

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length_a	54.245 Å
length_b	62.373 Å
length_c	88.442 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.000 Å
resolution_low	46.240 Å
r_factor	0.1902
r_work	0.1878
r_free	0.2358

fit	/app/data/saxs_computation/wq/9wqy/9wqy.fit
pddf	/app/data/pr_computation/wq/9wqy/9wqy.pr.out
profile	/app/data/saxs_computation/wq/9wqy/9wqy.dat

aminoacyl-tRNA-dependent peptide synthase, Sba18, complexed with streptothrisamine

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