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9y6d

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

Method: X-RAY DIFFRACTION D_max: 176.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y6d
deposition_date	2025-09-08
title	;CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR FORREST IN COMPLEX WITH PLP-GLYCINE ;
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	48.56 Å
rg_electron	48.94 Å
i0	899884000.00
molecular_weight	245110.0 kDa
excluded_volume	304770 Å³
envelope_volume	405040 Å³
shell_volume	72073 Å³
envelope_diameter	172.6 Å
shell_rg	49.43 Å
envelope_rg	49.17 Å
shape_rg	48.95 Å
total_rg	48.93 Å
total_atoms	17282
n_residues	2310
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	176.8 Å
rg_real	49.11 Å
rg_real_error	2.18 Å
i0_real	8.9990e+08
i0_real_error	1.7640e+07
rg_reciprocal	48.57 Å
i0_reciprocal	899200000.0000
total_estimate	0.7555
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.7 Å
skewness	0.570
kurtosis	-0.195
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	100100000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.673; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.800; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Serine hydroxymethyltransferase
formula_weight	54832.1 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	17890

MGMHHHHHHSSGVDLGTENLYFQSNMDPVSVWGNTPLATVDPEIHDLIEKEKRRQCRGIELIASENFTSFAVIEALGSALTNKYSEGMPGNRYYGGNEYIDQIENLCRSRALQAFHLDAQSWGVNVQPYSGSPANFAAYTAVLNPHDRIMGLDLRSGGHLTHGYYTSGGKKISTTSIYFESLPYKVNSTTGYIDYDRLEEKALDFRPKLIICGGSAYPRDWDYKRFREVADKCGALLLCDMAHTSGLVAAQEVNSPFEYCDIVTTTTHKSLRGPRAGMIFYRKGPKPPKKGQPENAVYDFEDKINFAVFPSLQGGPHNHQIGALAVALKQAASPGFKAYAKQVKANAVALGKYLMGKGYSLVTGGTENHLVLWDLRPLGLTGYKVEKLCDLCNITVNKNAVFGDSSALAPGGVRIGAPAMTSRGLVEKDFEQIGEFLHRAVTLTLEIQKEHGKLLKDFNKGLVNNKAIEDLKADVEKFSALFDMPGFLVSEMKYKD

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	608

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6. Citations (2)

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length_a	175.306 Å
length_b	175.306 Å
length_c	186.332 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	2.250 Å
resolution_low	48.860 Å
r_factor	0.2671
r_work	0.2648
r_free	0.3109

fit	/app/data/saxs_computation/y6/9y6d/9y6d.fit
pddf	/app/data/pr_computation/y6/9y6d/9y6d.pr.out
profile	/app/data/saxs_computation/y6/9y6d/9y6d.dat

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