CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP

Method: X-RAY DIFFRACTION D_max: 208.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ybz
deposition_date	2025-09-17
title	CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP
keywords	enzyme, missense variant, 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	61.22 Å
rg_electron	62.04 Å
i0	1205880000.00
molecular_weight	283730.0 kDa
excluded_volume	351500 Å³
envelope_volume	514790 Å³
shell_volume	76317 Å³
envelope_diameter	224.7 Å
shell_rg	53.61 Å
envelope_rg	63.73 Å
shape_rg	62.08 Å
total_rg	61.66 Å
total_atoms	20014
n_residues	2747
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	208.1 Å
rg_real	62.46 Å
rg_real_error	2.33 Å
i0_real	1.2060e+09
i0_real_error	2.6480e+07
rg_reciprocal	60.11 Å
i0_reciprocal	1201000000.0000
total_estimate	0.7384
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	48.0 Å
skewness	0.660
kurtosis	-0.338
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0001
highest_alpha	49410000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.574; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.781; Smooth: 0.093

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	174.318 Å
length_b	174.318 Å
length_c	184.208 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	36

space_group	P 31 2 1
int_tables_number	152
crystal_system	trigonal

resolution	2.280 Å
resolution_low	48.540 Å
r_factor	0.2742
r_work	0.2721
r_free	0.3128

description	Serine hydroxymethyltransferase
formula_weight	54951.1 kDa
ec_number	2.1.2.1
mutation	A149T
src_method	man
entity_count	6

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	20214

CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH 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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Glycine max
common_name	soybean
ncbi_taxonomy_id	3847
host_organism	Escherichia coli

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	199

fit	/app/data/saxs_computation/yb/9ybz/9ybz.fit
pddf	/app/data/pr_computation/yb/9ybz/9ybz.pr.out
profile	/app/data/saxs_computation/yb/9ybz/9ybz.dat