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

Method: X-RAY DIFFRACTION D_max: 207.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y7g
deposition_date	2025-09-10
title	CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR FORREST 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	62.12 Å
rg_electron	63.56 Å
i0	1281190000.00
molecular_weight	299060.0 kDa
excluded_volume	373410 Å³
envelope_volume	530480 Å³
shell_volume	77044 Å³
envelope_diameter	229.7 Å
shell_rg	54.31 Å
envelope_rg	64.74 Å
shape_rg	63.56 Å
total_rg	63.33 Å
total_atoms	21085
n_residues	2778
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	207.4 Å
rg_real	63.33 Å
rg_real_error	2.15 Å
i0_real	1.2810e+09
i0_real_error	2.6510e+07
rg_reciprocal	60.99 Å
i0_reciprocal	1276000000.0000
total_estimate	0.7437
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	41.5 Å
skewness	0.636
kurtosis	-0.399
angular_range	— – 0.1250 Å⁻¹
current_alpha	0.0007
highest_alpha	45700000.0000
n_real_points	26
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.614; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.743; Smooth: 0.081

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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	175.184 Å
length_b	175.184 Å
length_c	183.569 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	1.870 Å
resolution_low	48.750 Å
r_factor	0.2190
r_work	0.2172
r_free	0.2523

description	Serine hydroxymethyltransferase
formula_weight	55060.2 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	22130

CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR FORREST 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	1045

fit	/app/data/saxs_computation/y7/9y7g/9y7g.fit
pddf	/app/data/pr_computation/y7/9y7g/9y7g.pr.out
profile	/app/data/saxs_computation/y7/9y7g/9y7g.dat