← Back to search

9y6b

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

Method: X-RAY DIFFRACTION D_max: 176.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9y6b
deposition_date	2025-09-08
title	CRYSTAL STRUCTURE OF A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP-GLYCINE
keywords	enzyme, missense variant, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	47.98 Å
rg_electron	48.48 Å
i0	893572000.00
molecular_weight	245140.0 kDa
excluded_volume	305270 Å³
envelope_volume	394730 Å³
shell_volume	70906 Å³
envelope_diameter	189.6 Å
shell_rg	48.69 Å
envelope_rg	49.16 Å
shape_rg	48.48 Å
total_rg	48.51 Å
total_atoms	17282
n_residues	2299
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

▼

3. P(r) Analysis (GNOM)

dmax	176.9 Å
rg_real	48.58 Å
rg_real_error	2.20 Å
i0_real	8.9360e+08
i0_real_error	1.7000e+07
rg_reciprocal	47.98 Å
i0_reciprocal	892900000.0000
total_estimate	0.8086
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	48.3 Å
skewness	0.619
kurtosis	-0.074
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	116600000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.625; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.820; Smooth: 0.812

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Serine hydroxymethyltransferase
formula_weight	54723.0 kDa
ec_number	2.1.2.1
mutation	A149T
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	17910

MGMHHHHHHSSGVDLGTENLYFQSNMDPVSVWGNTPLATVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSALTNKYSEGMPGNRYYGGNEYIDQIENLCRSRALQAFHLDAQSWGVNVQPYSGSPANFAAYTAVLNPHDRIMGLDLPSGGHLTHGYYTSGGKKISTTSIYFESLPYKVNSTTGYIDYDRLEEKALDFRPKLIICGGSAYPRDWDYKRFREVADKCGALLLCDMAHTSGLVAAQEVNSPFEYCDIVTTTTHKSLRGPRAGMIFYRKGPKPPKKGQPENAVYDFEDKINFAVFPSLQGGPHNHQIGALAVALKQAASPGFKAYAKQVKANAVALGKYLMGKGYSLVTGGTENHLVLWDLRPLGLTGNKVEKLCDLCNITVNKNAVFGDSSALAPGGVRIGAPAMTSRGLVEKDFEQIGEFLHRAVTLTLEIQKEHGKLLKDFNKGLVNNKAIEDLKADVEKFSALFDMPGFLVSEMKYKD

Source

organism	Glycine max
common_name	soybean
ncbi_taxonomy_id	3847
host_organism	Escherichia coli

Entity 2 non-polymer

description	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
formula_weight	306.2 kDa
src_method	syn
entity_count	5

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	628

▶

6. Citations (1)

▶

length_a	174.351 Å
length_b	174.351 Å
length_c	183.632 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	30

space_group	P 31 2 1
int_tables_number	152
crystal_system	trigonal

resolution	1.900 Å
resolution_low	48.540 Å
r_factor	0.2841
r_work	0.2823
r_free	0.3193

fit	/app/data/saxs_computation/y6/9y6b/9y6b.fit
pddf	/app/data/pr_computation/y6/9y6b/9y6b.pr.out
profile	/app/data/saxs_computation/y6/9y6b/9y6b.dat

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

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