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9vgk

Ancestral L-tryptophan synthase beta-subunit 1 complex with Trp-PLP

Method: X-RAY DIFFRACTION D_max: 115.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vgk
deposition_date	2025-06-14
last_revision	2025-11-12
title	Ancestral L-tryptophan synthase beta-subunit 1 complex with Trp-PLP
keywords	L-tryptophan synthase beta-subunit, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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	36.70 Å
rg_electron	36.10 Å
i0	460934000.00
molecular_weight	173250.0 kDa
excluded_volume	216280 Å³
envelope_volume	262250 Å³
shell_volume	58595 Å³
envelope_diameter	123.8 Å
shell_rg	43.95 Å
envelope_rg	35.72 Å
shape_rg	36.09 Å
total_rg	36.60 Å
total_atoms	12148
n_residues	1556
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	115.8 Å
rg_real	36.53 Å
rg_real_error	0.89 Å
i0_real	4.6090e+08
i0_real_error	8.0340e+06
rg_reciprocal	36.64 Å
i0_reciprocal	461000000.0000
total_estimate	0.9002
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	51.1 Å
skewness	0.143
kurtosis	-0.572
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	464700000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.919

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Ancestral L-tyrptophan synthase beta-subunit 1 K90A
formula_weight	43894.0 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	12322

MKTYNVDENGYYGEFGGAYIPEILHKCVEDLQNNYLKILESPDFQKEYDQLLRDYVGRPSPLYLAKRLSEKYGCKIYLKREDLNHTGAHAINNTIGQILLARRMGKTRIIAETGAGQHGVATATVCALMNMECIVYMGKTDVERQHVNVQKMEMLGATVVPVTSGNMTLKDATNEAIRDWCCHPSDTYYIIGSTVGPHPYPDMVARLQSVISKEIKKQLQEKEGRDYPDYLIACVGGGSNAAGTIYHYIDDERVKIVLAEAGGKGIDSGMTAATIHLGKMGIIHGSKTLVMQNEDGQIEEPYSISAGLDYPGIGPMHANLAKQKRAQVLAINDDEALNAAFELTRLEGIIPALESAHALAALEKVKFKPEDVVVLTLSGRGDKDMETYLKYKKNSNE

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-tryptophan
formula_weight	433.4 kDa
src_method	syn
entity_count	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	174

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6. Citations (1)

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length_a	80.817 Å
length_b	100.339 Å
length_c	89.656 Å
angle_alpha	90.00 °
angle_beta	90.34 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.200 Å
resolution_low	42.620 Å
r_factor	0.1836
r_work	0.1804
r_free	0.2408

fit	/app/data/saxs_computation/vg/9vgk/9vgk.fit
pddf	/app/data/pr_computation/vg/9vgk/9vgk.pr.out
profile	/app/data/saxs_computation/vg/9vgk/9vgk.dat

Ancestral L-tryptophan synthase beta-subunit 1 complex with Trp-PLP

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