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9wqx

aminoacyl-tRNA-dependent peptide synthase, Sbb17, complexed with streptothrisamine

Method: X-RAY DIFFRACTION D_max: 68.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wqx
deposition_date	2025-09-11
title	aminoacyl-tRNA-dependent peptide synthase, Sbb17, complexed with streptothrisamine
keywords	aminoacyl-tRNA-dependent peptide synthase, Sbb17, 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	20.42 Å
rg_electron	19.63 Å
i0	32694900.00
molecular_weight	29218.0 kDa
excluded_volume	28125 Å³
envelope_volume	45669 Å³
shell_volume	19759 Å³
envelope_diameter	71.4 Å
shell_rg	25.74 Å
envelope_rg	19.83 Å
shape_rg	19.60 Å
total_rg	20.30 Å
total_atoms	2219
n_residues	286
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	68.0 Å
rg_real	20.41 Å
rg_real_error	0.44 Å
i0_real	3.2690e+07
i0_real_error	4.1300e+05
rg_reciprocal	20.41 Å
i0_reciprocal	32690000.0000
total_estimate	0.6141
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	24.3 Å
skewness	0.377
kurtosis	-0.225
angular_range	— – 0.3900 Å⁻¹
current_alpha	0.0000
highest_alpha	7371000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.803; Stabil: 0.998; Sysdev: 0.193; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	aminoacyl-tRNA-dependent peptide synthase
formula_weight	33965.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2320

MRGSHHHHHHGSACELLRLIMDPESTADAPEGADVPAEDFHQSAGRFRLLSGRGDPVRLLRAGRPGGRWAATLLEDGGQDGWFMWKGPAGLPDPELLSALLTGIAQLGPATLVLLPEWDFPEVLAAAGYRPGPPYATGLVPTGGGDEAILARMRPSTRSRVRRALRSGLEFADDPGRIDEFYDFYAPAMIRADSPDLAPLDLLHDLLEHSSVHLFTALHEDRVAAGSICFRNRNSLEARFVATHPDHRVDGSMNFVHFETIRRAAAEGLEYFDLSGISTGEVDEKTAGINRFKLGFGGEVLHYPTYTRSAG

Source

organism	Streptomyces prunicolor
ncbi_taxonomy_id	67348
host_organism	Escherichia coli M15

Entity 2 non-polymer

description	streptothrisamine
formula_weight	374.4 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	101

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6. Citations (1)

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length_a	63.066 Å
length_b	182.037 Å
length_c	71.292 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	orthorhombic

resolution	2.500 Å
resolution_low	45.510 Å
r_factor	0.1951
r_work	0.1929
r_free	0.2353

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

aminoacyl-tRNA-dependent peptide synthase, Sbb17, 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