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9x50

Crystal structure of Fgm3 in complex with PLP and L-Ala

Method: X-RAY DIFFRACTION D_max: 91.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x50
deposition_date	2025-10-12
last_revision	2026-05-20
title	Crystal structure of Fgm3 in complex with PLP and L-Ala
keywords	PLP, Retro-aldol-like, Cbeta-Cgamma Bond Cleavage, 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	27.89 Å
rg_electron	27.14 Å
i0	229405000.00
molecular_weight	81174.0 kDa
excluded_volume	78745 Å³
envelope_volume	125380 Å³
shell_volume	37639 Å³
envelope_diameter	95.2 Å
shell_rg	35.58 Å
envelope_rg	27.35 Å
shape_rg	27.10 Å
total_rg	27.77 Å
total_atoms	6170
n_residues	792
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	91.7 Å
rg_real	27.83 Å
rg_real_error	0.55 Å
i0_real	2.2940e+08
i0_real_error	3.2160e+06
rg_reciprocal	27.85 Å
i0_reciprocal	229400000.0000
total_estimate	0.8893
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.2 Å
skewness	0.322
kurtosis	-0.372
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	85790000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.987

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Aminotransferase-like protein FGM3
formula_weight	44835.4 kDa
ec_number	2.-.-.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6791

MSSSSFSIENVRSQFPALEKRQIFGDNAGGSQVLGTVAKSITEYLIETNVQLGASYKTSTQSTAIFDNAYKAAAKYINAGIDEIVIGASTTQVFRNLAAALKLQPGDELILTNVDHESNIDPWLHYAALNNATIKWWTPSDLNNPKLDPEQLRSLLTNKTRLVACTHCSNILGTINNIKAIADVVHEIPGALLAVDGVAYAPHRAIDVKELGADFYAFSWYKVYGPHISLLYGSKAAQAQLSSLGHFFNPDGSLMDKLELAAASYELTQAIIPLTAYFGENPKQTWDAIAEHEQKLQTRLIEYLVSKPQITVYGETSTDKAVRVPTVSFTVEGMSSQSVVEAVEAVSHAGIRWGHFFSKRLVGSILGLSDDGVVRVSLVHYNTVEEVDQIIVALEMVLLEHHHHHHHH

Source

organism	Fusarium graminearum PH-1
ncbi_taxonomy_id	229533
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid
formula_weight	316.2 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	621

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6. Citations (1)

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length_a	69.803 Å
length_b	98.013 Å
length_c	69.827 Å
angle_alpha	90.00 °
angle_beta	116.35 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.100 Å
resolution_low	36.810 Å
r_factor	0.1528
r_work	0.1513
r_free	0.1873

fit	/app/data/saxs_computation/x5/9x50/9x50.fit
pddf	/app/data/pr_computation/x5/9x50/9x50.pr.out
profile	/app/data/saxs_computation/x5/9x50/9x50.dat

Crystal structure of Fgm3 in complex with PLP and L-Ala

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